Starting phenix.real_space_refine on Thu Jul 24 19:56:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x8y_33060/07_2025/7x8y_33060_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8y_33060/07_2025/7x8y_33060.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/7x8y_33060/07_2025/7x8y_33060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8y_33060/07_2025/7x8y_33060.map" model { file = "/net/cci-nas-00/data/ceres_data/7x8y_33060/07_2025/7x8y_33060_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8y_33060/07_2025/7x8y_33060_trim.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2183 2.51 5 N 575 2.21 5 O 662 1.98 5 H 3296 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 6731 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3222 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "H" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1865 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "L" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1630 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.90, per 1000 atoms: 0.58 Number of scatterers: 6731 At special positions: 0 Unit cell: (61.346, 72.952, 120.205, 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 662 8.00 N 575 7.00 C 2183 6.00 H 3296 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=2.04 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 98 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 724.8 milliseconds 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 802 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 9.8% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.482A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.637A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.166A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 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 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 61 through 62 removed outlier: 3.529A pdb=" N ARG H 50 " --> pdb=" O ASP H 61 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) 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 53 through 54 removed outlier: 3.530A pdb=" N SER L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 2.29 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: 3296 1.04 - 1.24: 458 1.24 - 1.44: 1136 1.44 - 1.64: 1910 1.64 - 1.84: 18 Bond restraints: 6818 Sorted by residual: bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N GLN H 1 " pdb=" H GLN H 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" N ASP L 1 " pdb=" H ASP L 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 6813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 11371 1.03 - 2.06: 794 2.06 - 3.08: 44 3.08 - 4.11: 17 4.11 - 5.14: 3 Bond angle restraints: 12229 Sorted by residual: angle pdb=" N GLY H 26 " pdb=" CA GLY H 26 " pdb=" C GLY H 26 " ideal model delta sigma weight residual 114.16 119.30 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" N GLY H 57 " pdb=" CA GLY H 57 " pdb=" C GLY H 57 " ideal model delta sigma weight residual 114.48 111.74 2.74 1.19e+00 7.06e-01 5.31e+00 angle pdb=" CB ARG A 346 " pdb=" CG ARG A 346 " pdb=" CD ARG A 346 " ideal model delta sigma weight residual 111.30 115.18 -3.88 2.30e+00 1.89e-01 2.84e+00 angle pdb=" CG ARG A 346 " pdb=" CD ARG A 346 " pdb=" NE ARG A 346 " ideal model delta sigma weight residual 112.00 115.56 -3.56 2.20e+00 2.07e-01 2.62e+00 angle pdb=" CA GLN H 1 " pdb=" N GLN H 1 " pdb=" H GLN H 1 " ideal model delta sigma weight residual 114.00 109.44 4.56 3.00e+00 1.11e-01 2.31e+00 ... (remaining 12224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 2917 16.28 - 32.56: 282 32.56 - 48.83: 74 48.83 - 65.11: 25 65.11 - 81.39: 7 Dihedral angle restraints: 3305 sinusoidal: 1760 harmonic: 1545 Sorted by residual: 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 20.07 72.93 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CA GLY H 26 " pdb=" C GLY H 26 " pdb=" N PHE H 27 " pdb=" CA PHE H 27 " ideal model delta harmonic sigma weight residual 180.00 157.37 22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA SER H 25 " pdb=" C SER H 25 " pdb=" N GLY H 26 " pdb=" CA GLY H 26 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 3302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 292 0.027 - 0.053: 156 0.053 - 0.080: 35 0.080 - 0.107: 26 0.107 - 0.133: 12 Chirality restraints: 521 Sorted by residual: chirality pdb=" CA VAL H 2 " pdb=" N VAL H 2 " pdb=" C VAL H 2 " pdb=" CB VAL H 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL A 362 " pdb=" N VAL A 362 " pdb=" C VAL A 362 " pdb=" CB VAL A 362 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 518 not shown) Planarity restraints: 1031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " 0.096 9.50e-02 1.11e+02 3.22e-02 1.24e+00 pdb=" NE ARG A 408 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 408 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 408 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 408 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 408 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 346 " -0.079 9.50e-02 1.11e+02 2.68e-02 1.15e+00 pdb=" NE ARG A 346 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 346 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 346 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 346 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 346 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 346 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 346 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 346 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 112 " 0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO H 113 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO H 113 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 113 " 0.014 5.00e-02 4.00e+02 ... (remaining 1028 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 610 2.21 - 2.81: 13812 2.81 - 3.41: 16511 3.41 - 4.00: 21961 4.00 - 4.60: 32493 Nonbonded interactions: 85387 Sorted by model distance: nonbonded pdb=" H LYS A 462 " pdb=" OE2 GLU A 465 " model vdw 1.617 2.450 nonbonded pdb=" OE1 GLN L 55 " pdb=" H GLY L 56 " model vdw 1.631 2.450 nonbonded pdb=" HZ2 LYS A 444 " pdb=" O GLY A 447 " model vdw 1.648 2.450 nonbonded pdb=" O SER H 112 " pdb=" HE1 TRP H 115 " model vdw 1.678 2.450 nonbonded pdb=" OD1 ASN A 422 " pdb=" H ARG A 454 " model vdw 1.694 2.450 ... (remaining 85382 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: 0.260 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: 0.140 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.640 Find NCS groups from input model: 0.050 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:3.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 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 3529 Z= 0.122 Angle : 0.534 5.138 4802 Z= 0.285 Chirality : 0.040 0.133 521 Planarity : 0.004 0.042 615 Dihedral : 14.084 81.388 1267 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % 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: -3.09 (0.38), residues: 434 helix: -4.37 (0.55), residues: 26 sheet: -1.42 (0.44), residues: 133 loop : -2.23 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.016 0.001 PHE L 71 TYR 0.013 0.001 TYR L 36 ARG 0.010 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 1) link_NAG-ASN : angle 1.24968 ( 3) hydrogen bonds : bond 0.15057 ( 87) hydrogen bonds : angle 8.86800 ( 207) SS BOND : bond 0.00594 ( 6) SS BOND : angle 1.40232 ( 12) covalent geometry : bond 0.00260 ( 3522) covalent geometry : angle 0.52887 ( 4787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.674 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: H 45 LEU cc_start: 0.8460 (pt) cc_final: 0.8244 (pt) REVERT: H 56 ASP cc_start: 0.5517 (t0) cc_final: 0.5221 (t0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.5836 time to fit residues: 50.7229 Evaluate side-chains 42 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.0270 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.052222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.040296 restraints weight = 71928.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042373 restraints weight = 31145.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.043761 restraints weight = 17258.996| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3529 Z= 0.144 Angle : 0.521 4.895 4802 Z= 0.281 Chirality : 0.039 0.138 521 Planarity : 0.004 0.037 615 Dihedral : 5.086 42.734 504 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.37), residues: 434 helix: -4.24 (0.48), residues: 32 sheet: -0.97 (0.48), residues: 117 loop : -2.19 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.015 0.001 PHE L 71 TYR 0.006 0.001 TYR A 473 ARG 0.004 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00009 ( 1) link_NAG-ASN : angle 1.22308 ( 3) hydrogen bonds : bond 0.04060 ( 87) hydrogen bonds : angle 7.60903 ( 207) SS BOND : bond 0.00930 ( 6) SS BOND : angle 1.12456 ( 12) covalent geometry : bond 0.00301 ( 3522) covalent geometry : angle 0.51768 ( 4787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 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: A 528 LYS cc_start: 0.9673 (mppt) cc_final: 0.9339 (mmtt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.5356 time to fit residues: 33.5052 Evaluate side-chains 34 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 38 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.050069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.038639 restraints weight = 76959.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040605 restraints weight = 32818.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.041930 restraints weight = 18071.908| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3529 Z= 0.209 Angle : 0.554 5.030 4802 Z= 0.301 Chirality : 0.040 0.137 521 Planarity : 0.004 0.034 615 Dihedral : 4.926 32.423 504 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: -2.92 (0.38), residues: 434 helix: -4.30 (0.48), residues: 33 sheet: -1.09 (0.47), residues: 122 loop : -2.12 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.029 0.002 PHE A 392 TYR 0.013 0.001 TYR A 508 ARG 0.003 0.001 ARG L 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00017 ( 1) link_NAG-ASN : angle 1.26515 ( 3) hydrogen bonds : bond 0.03887 ( 87) hydrogen bonds : angle 7.73687 ( 207) SS BOND : bond 0.00365 ( 6) SS BOND : angle 0.93656 ( 12) covalent geometry : bond 0.00432 ( 3522) covalent geometry : angle 0.55213 ( 4787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.536 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: A 528 LYS cc_start: 0.9678 (mppt) cc_final: 0.9411 (mmtm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.4895 time to fit residues: 24.5393 Evaluate side-chains 27 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN H 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.050116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.038585 restraints weight = 74771.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.040582 restraints weight = 31636.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.041920 restraints weight = 17386.041| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3529 Z= 0.139 Angle : 0.511 4.428 4802 Z= 0.273 Chirality : 0.040 0.136 521 Planarity : 0.004 0.035 615 Dihedral : 4.508 22.542 504 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -2.71 (0.39), residues: 434 helix: -3.80 (0.65), residues: 31 sheet: -1.18 (0.47), residues: 122 loop : -1.92 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.012 0.001 PHE L 71 TYR 0.010 0.001 TYR L 36 ARG 0.002 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 1) link_NAG-ASN : angle 0.92080 ( 3) hydrogen bonds : bond 0.03505 ( 87) hydrogen bonds : angle 7.40392 ( 207) SS BOND : bond 0.00342 ( 6) SS BOND : angle 1.34578 ( 12) covalent geometry : bond 0.00295 ( 3522) covalent geometry : angle 0.50693 ( 4787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.9678 (mppt) cc_final: 0.9406 (mmtm) REVERT: H 56 ASP cc_start: 0.8686 (t0) cc_final: 0.8418 (t0) REVERT: L 97 THR cc_start: 0.8340 (m) cc_final: 0.7702 (m) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.4928 time to fit residues: 26.4629 Evaluate side-chains 28 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.048605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.037545 restraints weight = 78364.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.039468 restraints weight = 33256.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.040764 restraints weight = 18200.666| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3529 Z= 0.185 Angle : 0.529 4.665 4802 Z= 0.285 Chirality : 0.039 0.135 521 Planarity : 0.004 0.038 615 Dihedral : 4.516 21.960 504 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: -2.57 (0.39), residues: 434 helix: -3.01 (0.95), residues: 25 sheet: -1.27 (0.47), residues: 119 loop : -1.86 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 96 HIS 0.001 0.001 HIS A 519 PHE 0.014 0.002 PHE L 71 TYR 0.010 0.001 TYR A 508 ARG 0.002 0.001 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 1) link_NAG-ASN : angle 1.09612 ( 3) hydrogen bonds : bond 0.03363 ( 87) hydrogen bonds : angle 7.36972 ( 207) SS BOND : bond 0.00427 ( 6) SS BOND : angle 1.25250 ( 12) covalent geometry : bond 0.00386 ( 3522) covalent geometry : angle 0.52522 ( 4787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.9686 (mppt) cc_final: 0.9422 (mmtm) REVERT: H 56 ASP cc_start: 0.8803 (t0) cc_final: 0.8513 (t0) REVERT: L 97 THR cc_start: 0.8390 (m) cc_final: 0.7775 (m) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.4877 time to fit residues: 24.4316 Evaluate side-chains 31 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 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 = 0.3307 r_free = 0.3307 target = 0.048858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.037757 restraints weight = 78976.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.039724 restraints weight = 33470.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041042 restraints weight = 18242.191| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3529 Z= 0.163 Angle : 0.526 4.350 4802 Z= 0.281 Chirality : 0.039 0.133 521 Planarity : 0.004 0.052 615 Dihedral : 4.536 22.312 504 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.40), residues: 434 helix: -2.95 (0.98), residues: 25 sheet: -1.17 (0.48), residues: 118 loop : -1.80 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 35 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE A 392 TYR 0.010 0.001 TYR A 508 ARG 0.006 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 1) link_NAG-ASN : angle 1.02204 ( 3) hydrogen bonds : bond 0.03284 ( 87) hydrogen bonds : angle 7.26433 ( 207) SS BOND : bond 0.00380 ( 6) SS BOND : angle 1.56212 ( 12) covalent geometry : bond 0.00343 ( 3522) covalent geometry : angle 0.52082 ( 4787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.9662 (mppt) cc_final: 0.9299 (mmtt) REVERT: H 56 ASP cc_start: 0.8863 (t0) cc_final: 0.8606 (t0) REVERT: L 97 THR cc_start: 0.8401 (m) cc_final: 0.7863 (m) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.4725 time to fit residues: 24.7771 Evaluate side-chains 31 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 0.0070 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 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 = 0.3348 r_free = 0.3348 target = 0.049452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.038739 restraints weight = 75921.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.040669 restraints weight = 32362.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.041946 restraints weight = 17645.890| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3529 Z= 0.137 Angle : 0.516 4.551 4802 Z= 0.275 Chirality : 0.040 0.146 521 Planarity : 0.004 0.038 615 Dihedral : 4.505 22.498 504 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -2.58 (0.39), residues: 434 helix: -3.01 (0.80), residues: 31 sheet: -1.24 (0.47), residues: 122 loop : -1.84 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE L 71 TYR 0.017 0.001 TYR A 508 ARG 0.007 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 1) link_NAG-ASN : angle 1.13607 ( 3) hydrogen bonds : bond 0.03212 ( 87) hydrogen bonds : angle 7.14257 ( 207) SS BOND : bond 0.00361 ( 6) SS BOND : angle 1.18953 ( 12) covalent geometry : bond 0.00299 ( 3522) covalent geometry : angle 0.51276 ( 4787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9647 (mt) cc_final: 0.9349 (tp) REVERT: A 528 LYS cc_start: 0.9656 (mppt) cc_final: 0.9267 (mmtt) REVERT: H 56 ASP cc_start: 0.8923 (t0) cc_final: 0.8676 (t0) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.5227 time to fit residues: 27.7462 Evaluate side-chains 31 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 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 = 0.3329 r_free = 0.3329 target = 0.048662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.038007 restraints weight = 78713.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.039905 restraints weight = 33210.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.041170 restraints weight = 18051.283| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3529 Z= 0.200 Angle : 0.547 4.170 4802 Z= 0.294 Chirality : 0.039 0.133 521 Planarity : 0.004 0.044 615 Dihedral : 4.723 22.460 504 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.40), residues: 434 helix: -2.55 (0.95), residues: 25 sheet: -1.24 (0.46), residues: 128 loop : -1.81 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 35 HIS 0.002 0.001 HIS A 519 PHE 0.009 0.002 PHE L 71 TYR 0.014 0.001 TYR A 508 ARG 0.006 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 1) link_NAG-ASN : angle 1.23090 ( 3) hydrogen bonds : bond 0.03441 ( 87) hydrogen bonds : angle 7.42346 ( 207) SS BOND : bond 0.00340 ( 6) SS BOND : angle 1.41587 ( 12) covalent geometry : bond 0.00417 ( 3522) covalent geometry : angle 0.54234 ( 4787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.9402 (m-10) cc_final: 0.9201 (m-10) REVERT: A 434 ILE cc_start: 0.9659 (mt) cc_final: 0.9364 (tp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.5980 time to fit residues: 27.2221 Evaluate side-chains 32 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 0.0060 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 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 = 0.3328 r_free = 0.3328 target = 0.049008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.038047 restraints weight = 79458.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040017 restraints weight = 33995.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.041323 restraints weight = 18491.394| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3529 Z= 0.121 Angle : 0.503 4.041 4802 Z= 0.268 Chirality : 0.040 0.135 521 Planarity : 0.004 0.035 615 Dihedral : 4.480 22.441 504 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.40), residues: 434 helix: -2.40 (0.97), residues: 25 sheet: -1.17 (0.48), residues: 125 loop : -1.73 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE A 392 TYR 0.014 0.001 TYR A 508 ARG 0.006 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 1) link_NAG-ASN : angle 1.11940 ( 3) hydrogen bonds : bond 0.03021 ( 87) hydrogen bonds : angle 7.16659 ( 207) SS BOND : bond 0.00512 ( 6) SS BOND : angle 1.39777 ( 12) covalent geometry : bond 0.00270 ( 3522) covalent geometry : angle 0.49827 ( 4787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9644 (mt) cc_final: 0.9331 (tp) REVERT: A 528 LYS cc_start: 0.9663 (mppt) cc_final: 0.9398 (mmtm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.7340 time to fit residues: 33.7544 Evaluate side-chains 30 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 30.0000 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 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 = 0.3333 r_free = 0.3333 target = 0.048987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.037849 restraints weight = 79785.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.039835 restraints weight = 33613.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.041162 restraints weight = 18279.551| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3529 Z= 0.111 Angle : 0.492 4.186 4802 Z= 0.261 Chirality : 0.039 0.136 521 Planarity : 0.004 0.034 615 Dihedral : 4.283 21.610 504 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.40), residues: 434 helix: -2.42 (0.98), residues: 25 sheet: -1.26 (0.47), residues: 125 loop : -1.67 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.001 PHE A 392 TYR 0.013 0.001 TYR A 508 ARG 0.005 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 1) link_NAG-ASN : angle 1.16959 ( 3) hydrogen bonds : bond 0.02926 ( 87) hydrogen bonds : angle 6.94737 ( 207) SS BOND : bond 0.00586 ( 6) SS BOND : angle 1.20168 ( 12) covalent geometry : bond 0.00252 ( 3522) covalent geometry : angle 0.48845 ( 4787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9636 (mt) cc_final: 0.9305 (tp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.6308 time to fit residues: 28.8323 Evaluate side-chains 31 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 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 = 0.3318 r_free = 0.3318 target = 0.048389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.037275 restraints weight = 79387.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.039226 restraints weight = 33308.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.040507 restraints weight = 18090.251| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3529 Z= 0.151 Angle : 0.504 3.896 4802 Z= 0.272 Chirality : 0.039 0.135 521 Planarity : 0.005 0.062 615 Dihedral : 4.414 21.557 504 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.41), residues: 434 helix: -2.12 (1.08), residues: 25 sheet: -1.03 (0.47), residues: 129 loop : -1.61 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 35 HIS 0.002 0.001 HIS A 519 PHE 0.009 0.002 PHE A 392 TYR 0.013 0.001 TYR A 508 ARG 0.005 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 1) link_NAG-ASN : angle 1.20083 ( 3) hydrogen bonds : bond 0.03197 ( 87) hydrogen bonds : angle 6.93173 ( 207) SS BOND : bond 0.00608 ( 6) SS BOND : angle 1.37338 ( 12) covalent geometry : bond 0.00326 ( 3522) covalent geometry : angle 0.49966 ( 4787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3054.40 seconds wall clock time: 55 minutes 16.37 seconds (3316.37 seconds total)