Starting phenix.real_space_refine on Fri May 9 18:10:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wp2_32667/05_2025/7wp2_32667.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp2_32667/05_2025/7wp2_32667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wp2_32667/05_2025/7wp2_32667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp2_32667/05_2025/7wp2_32667.map" model { file = "/net/cci-nas-00/data/ceres_data/7wp2_32667/05_2025/7wp2_32667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp2_32667/05_2025/7wp2_32667.cif" } resolution = 3.52 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= 0.011 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2090 2.51 5 N 554 2.21 5 O 641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3299 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "F" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1458 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} 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: 5.34, per 1000 atoms: 1.62 Number of scatterers: 3299 At special positions: 0 Unit cell: (76.244, 79.356, 80.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 641 8.00 N 554 7.00 C 2090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " 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 F 343 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 9 sheets defined 2.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.905A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.037A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.623A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'L' and resid 22 through 23 removed outlier: 3.520A pdb=" N SER L 69 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.564A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 89 " --> pdb=" O TYR L 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.785A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.880A pdb=" N ASN F 354 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER F 399 " --> pdb=" O ASN F 354 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS F 356 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 452 through 454 69 hydrogen bonds defined for protein. 159 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: 0.88 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1049 1.34 - 1.46: 843 1.46 - 1.57: 1473 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3383 Sorted by residual: bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" C LYS F 462 " pdb=" N PRO F 463 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 3.02e+00 bond pdb=" CB CYS L 90 " pdb=" SG CYS L 90 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" C ASN L 55 " pdb=" N ARG L 56 " ideal model delta sigma weight residual 1.332 1.271 0.060 3.60e-02 7.72e+02 2.81e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 3378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 4496 2.54 - 5.07: 85 5.07 - 7.61: 9 7.61 - 10.15: 3 10.15 - 12.69: 1 Bond angle restraints: 4594 Sorted by residual: angle pdb=" C GLY L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" CA LEU F 387 " pdb=" CB LEU F 387 " pdb=" CG LEU F 387 " ideal model delta sigma weight residual 116.30 128.99 -12.69 3.50e+00 8.16e-02 1.31e+01 angle pdb=" C TYR F 369 " pdb=" N ASN F 370 " pdb=" CA ASN F 370 " ideal model delta sigma weight residual 122.07 127.10 -5.03 1.43e+00 4.89e-01 1.24e+01 angle pdb=" C ASP F 364 " pdb=" N TYR F 365 " pdb=" CA TYR F 365 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.58e+00 angle pdb=" C SER H 52 " pdb=" N PHE H 53 " pdb=" CA PHE H 53 " ideal model delta sigma weight residual 120.44 124.43 -3.99 1.30e+00 5.92e-01 9.40e+00 ... (remaining 4589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 1779 17.78 - 35.55: 173 35.55 - 53.33: 25 53.33 - 71.11: 5 71.11 - 88.88: 3 Dihedral angle restraints: 1985 sinusoidal: 780 harmonic: 1205 Sorted by residual: dihedral pdb=" CA ASP H 113 " pdb=" C ASP H 113 " pdb=" N TYR H 114 " pdb=" CA TYR H 114 " ideal model delta harmonic sigma weight residual -180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PHE F 338 " pdb=" C PHE F 338 " pdb=" N GLY F 339 " pdb=" CA GLY F 339 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ILE F 472 " pdb=" C ILE F 472 " pdb=" N TYR F 473 " pdb=" CA TYR F 473 " ideal model delta harmonic sigma weight residual 180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 1982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 306 0.047 - 0.094: 137 0.094 - 0.141: 34 0.141 - 0.188: 7 0.188 - 0.235: 5 Chirality restraints: 489 Sorted by residual: chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB THR H 91 " pdb=" CA THR H 91 " pdb=" OG1 THR H 91 " pdb=" CG2 THR H 91 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL H 100 " pdb=" CA VAL H 100 " pdb=" CG1 VAL H 100 " pdb=" CG2 VAL H 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 486 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 498 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO F 499 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 499 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 499 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 13 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO L 14 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 462 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO F 463 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 463 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 463 " -0.027 5.00e-02 4.00e+02 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 909 2.79 - 3.32: 2630 3.32 - 3.85: 5262 3.85 - 4.37: 5959 4.37 - 4.90: 10778 Nonbonded interactions: 25538 Sorted by model distance: nonbonded pdb=" OH TYR L 93 " pdb=" OD1 ASP H 113 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR F 415 " pdb=" OD1 ASP F 420 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR L 38 " pdb=" OE1 GLN L 91 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR L 51 " pdb=" O THR F 415 " model vdw 2.280 3.040 nonbonded pdb=" NE2 HIS L 36 " pdb=" O ASN H 115 " model vdw 2.288 3.120 ... (remaining 25533 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=0.00 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: 10.860 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.200 Find NCS groups from input model: 0.040 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.007 0.060 3387 Z= 0.304 Angle : 0.911 12.687 4604 Z= 0.500 Chirality : 0.056 0.235 489 Planarity : 0.007 0.070 594 Dihedral : 13.822 88.882 1225 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.28 % Allowed : 9.66 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.34), residues: 416 helix: -5.07 (0.26), residues: 20 sheet: -2.60 (0.38), residues: 162 loop : -3.28 (0.31), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 353 HIS 0.004 0.002 HIS F 449 PHE 0.018 0.002 PHE F 490 TYR 0.028 0.003 TYR H 103 ARG 0.005 0.000 ARG F 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 1) link_NAG-ASN : angle 2.65504 ( 3) link_BETA1-4 : bond 0.00720 ( 1) link_BETA1-4 : angle 1.70846 ( 3) hydrogen bonds : bond 0.26493 ( 69) hydrogen bonds : angle 10.34313 ( 159) SS BOND : bond 0.00311 ( 2) SS BOND : angle 1.70877 ( 4) covalent geometry : bond 0.00700 ( 3383) covalent geometry : angle 0.90724 ( 4594) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.379 Fit side-chains REVERT: L 93 TYR cc_start: 0.8650 (t80) cc_final: 0.8437 (t80) REVERT: H 19 ARG cc_start: 0.7666 (ttm170) cc_final: 0.6860 (ttp80) REVERT: H 29 PHE cc_start: 0.9274 (t80) cc_final: 0.9067 (t80) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.1927 time to fit residues: 17.5952 Evaluate side-chains 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 17 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 ASN F 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131603 restraints weight = 4660.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134857 restraints weight = 2488.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137020 restraints weight = 1632.163| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3387 Z= 0.154 Angle : 0.601 7.885 4604 Z= 0.313 Chirality : 0.043 0.139 489 Planarity : 0.005 0.047 594 Dihedral : 6.820 54.457 516 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.99 % Allowed : 14.77 % Favored : 83.24 % 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: -3.96 (0.35), residues: 416 helix: -4.82 (0.44), residues: 20 sheet: -1.92 (0.40), residues: 151 loop : -3.01 (0.33), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 353 HIS 0.003 0.001 HIS L 36 PHE 0.013 0.001 PHE F 338 TYR 0.012 0.001 TYR H 103 ARG 0.005 0.001 ARG L 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 1) link_NAG-ASN : angle 1.46339 ( 3) link_BETA1-4 : bond 0.00444 ( 1) link_BETA1-4 : angle 1.08267 ( 3) hydrogen bonds : bond 0.04417 ( 69) hydrogen bonds : angle 7.33011 ( 159) SS BOND : bond 0.00227 ( 2) SS BOND : angle 1.26197 ( 4) covalent geometry : bond 0.00371 ( 3383) covalent geometry : angle 0.59887 ( 4594) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.362 Fit side-chains REVERT: L 93 TYR cc_start: 0.8681 (t80) cc_final: 0.8396 (t80) REVERT: H 19 ARG cc_start: 0.7612 (ttm170) cc_final: 0.6966 (ttp80) REVERT: F 417 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7665 (ttmm) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.1702 time to fit residues: 13.1363 Evaluate side-chains 58 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.153265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136055 restraints weight = 4520.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139403 restraints weight = 2450.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141622 restraints weight = 1621.499| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3387 Z= 0.179 Angle : 0.603 7.919 4604 Z= 0.311 Chirality : 0.043 0.142 489 Planarity : 0.004 0.037 594 Dihedral : 6.455 48.872 516 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.83 % Allowed : 14.49 % Favored : 80.68 % 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: -3.73 (0.36), residues: 416 helix: -4.72 (0.49), residues: 20 sheet: -1.79 (0.41), residues: 150 loop : -2.82 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 353 HIS 0.003 0.002 HIS F 449 PHE 0.016 0.002 PHE F 338 TYR 0.012 0.001 TYR H 94 ARG 0.007 0.001 ARG F 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 1) link_NAG-ASN : angle 1.60088 ( 3) link_BETA1-4 : bond 0.00343 ( 1) link_BETA1-4 : angle 0.98361 ( 3) hydrogen bonds : bond 0.03592 ( 69) hydrogen bonds : angle 6.44311 ( 159) SS BOND : bond 0.00273 ( 2) SS BOND : angle 1.26827 ( 4) covalent geometry : bond 0.00437 ( 3383) covalent geometry : angle 0.60104 ( 4594) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.334 Fit side-chains REVERT: L 93 TYR cc_start: 0.8707 (t80) cc_final: 0.8399 (t80) REVERT: H 19 ARG cc_start: 0.7651 (ttm170) cc_final: 0.7259 (ttp-170) REVERT: H 94 TYR cc_start: 0.8169 (m-80) cc_final: 0.7412 (m-80) REVERT: F 338 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.6691 (p90) REVERT: F 417 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7683 (ttmm) outliers start: 17 outliers final: 9 residues processed: 73 average time/residue: 0.1584 time to fit residues: 14.0305 Evaluate side-chains 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.0470 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 30 optimal weight: 0.0570 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132959 restraints weight = 4646.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.136042 restraints weight = 2587.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138077 restraints weight = 1731.270| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3387 Z= 0.124 Angle : 0.578 7.307 4604 Z= 0.295 Chirality : 0.042 0.137 489 Planarity : 0.004 0.034 594 Dihedral : 5.901 45.014 516 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.83 % Allowed : 15.06 % Favored : 80.11 % 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: -3.48 (0.37), residues: 416 helix: -4.66 (0.52), residues: 20 sheet: -1.65 (0.41), residues: 148 loop : -2.61 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 353 HIS 0.002 0.001 HIS H 35 PHE 0.016 0.001 PHE H 53 TYR 0.012 0.001 TYR F 369 ARG 0.004 0.000 ARG F 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 1) link_NAG-ASN : angle 1.14719 ( 3) link_BETA1-4 : bond 0.00386 ( 1) link_BETA1-4 : angle 0.88042 ( 3) hydrogen bonds : bond 0.03067 ( 69) hydrogen bonds : angle 6.23686 ( 159) SS BOND : bond 0.00188 ( 2) SS BOND : angle 1.03855 ( 4) covalent geometry : bond 0.00305 ( 3383) covalent geometry : angle 0.57659 ( 4594) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.324 Fit side-chains REVERT: L 93 TYR cc_start: 0.8651 (t80) cc_final: 0.8388 (t80) REVERT: H 19 ARG cc_start: 0.7637 (ttm170) cc_final: 0.6997 (ttp80) REVERT: H 94 TYR cc_start: 0.8136 (m-80) cc_final: 0.7463 (m-80) outliers start: 17 outliers final: 11 residues processed: 67 average time/residue: 0.1542 time to fit residues: 12.6834 Evaluate side-chains 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.0470 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.3634 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.149404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132454 restraints weight = 4645.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135701 restraints weight = 2480.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137780 restraints weight = 1631.898| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3387 Z= 0.128 Angle : 0.569 6.972 4604 Z= 0.290 Chirality : 0.042 0.139 489 Planarity : 0.003 0.032 594 Dihedral : 5.613 41.852 516 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.69 % Allowed : 15.91 % Favored : 80.40 % 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: -3.25 (0.37), residues: 416 helix: -4.60 (0.55), residues: 20 sheet: -1.45 (0.43), residues: 143 loop : -2.46 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 353 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.001 PHE H 53 TYR 0.011 0.001 TYR F 369 ARG 0.003 0.000 ARG F 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 1) link_NAG-ASN : angle 1.19579 ( 3) link_BETA1-4 : bond 0.00431 ( 1) link_BETA1-4 : angle 0.87861 ( 3) hydrogen bonds : bond 0.02966 ( 69) hydrogen bonds : angle 6.13279 ( 159) SS BOND : bond 0.00190 ( 2) SS BOND : angle 1.53489 ( 4) covalent geometry : bond 0.00313 ( 3383) covalent geometry : angle 0.56608 ( 4594) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.338 Fit side-chains REVERT: L 93 TYR cc_start: 0.8701 (t80) cc_final: 0.8438 (t80) REVERT: H 19 ARG cc_start: 0.7685 (ttm170) cc_final: 0.6868 (ttp80) REVERT: H 94 TYR cc_start: 0.8171 (m-80) cc_final: 0.7438 (m-80) REVERT: F 338 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6543 (p90) REVERT: F 386 LYS cc_start: 0.8108 (tmtt) cc_final: 0.7755 (mttp) REVERT: F 454 ARG cc_start: 0.8853 (tpp80) cc_final: 0.8392 (ttm-80) outliers start: 13 outliers final: 11 residues processed: 64 average time/residue: 0.1610 time to fit residues: 12.6032 Evaluate side-chains 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.151730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134803 restraints weight = 4660.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138066 restraints weight = 2447.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140257 restraints weight = 1601.184| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3387 Z= 0.215 Angle : 0.634 8.604 4604 Z= 0.321 Chirality : 0.044 0.146 489 Planarity : 0.004 0.033 594 Dihedral : 5.875 41.345 516 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 4.26 % Allowed : 15.34 % Favored : 80.40 % 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: -3.22 (0.38), residues: 416 helix: -4.70 (0.47), residues: 20 sheet: -1.44 (0.43), residues: 146 loop : -2.43 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 353 HIS 0.003 0.002 HIS H 35 PHE 0.017 0.002 PHE F 338 TYR 0.012 0.002 TYR H 94 ARG 0.004 0.001 ARG F 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 1) link_NAG-ASN : angle 1.66010 ( 3) link_BETA1-4 : bond 0.00244 ( 1) link_BETA1-4 : angle 0.89336 ( 3) hydrogen bonds : bond 0.03327 ( 69) hydrogen bonds : angle 6.05600 ( 159) SS BOND : bond 0.00418 ( 2) SS BOND : angle 1.42669 ( 4) covalent geometry : bond 0.00534 ( 3383) covalent geometry : angle 0.63098 ( 4594) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.372 Fit side-chains REVERT: L 93 TYR cc_start: 0.8730 (t80) cc_final: 0.8424 (t80) REVERT: L 94 ASP cc_start: 0.6718 (t0) cc_final: 0.6433 (t0) REVERT: H 19 ARG cc_start: 0.7517 (ttm170) cc_final: 0.6901 (ttp80) REVERT: H 94 TYR cc_start: 0.8291 (m-80) cc_final: 0.7480 (m-80) REVERT: F 338 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.6962 (p90) REVERT: F 386 LYS cc_start: 0.8169 (tmtt) cc_final: 0.7800 (mttp) outliers start: 15 outliers final: 13 residues processed: 67 average time/residue: 0.1471 time to fit residues: 12.2366 Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.152357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134722 restraints weight = 4591.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138011 restraints weight = 2495.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140205 restraints weight = 1669.977| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 3387 Z= 0.214 Angle : 0.631 7.432 4604 Z= 0.322 Chirality : 0.044 0.164 489 Planarity : 0.004 0.048 594 Dihedral : 5.951 42.137 516 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 4.55 % Allowed : 15.91 % Favored : 79.55 % 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: -3.23 (0.38), residues: 416 helix: -4.80 (0.38), residues: 20 sheet: -1.52 (0.43), residues: 146 loop : -2.38 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 353 HIS 0.003 0.002 HIS H 35 PHE 0.017 0.002 PHE F 338 TYR 0.016 0.002 TYR F 369 ARG 0.003 0.001 ARG F 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 1) link_NAG-ASN : angle 1.71421 ( 3) link_BETA1-4 : bond 0.00365 ( 1) link_BETA1-4 : angle 0.94184 ( 3) hydrogen bonds : bond 0.03286 ( 69) hydrogen bonds : angle 6.05140 ( 159) SS BOND : bond 0.00469 ( 2) SS BOND : angle 1.26916 ( 4) covalent geometry : bond 0.00532 ( 3383) covalent geometry : angle 0.62819 ( 4594) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.338 Fit side-chains REVERT: L 93 TYR cc_start: 0.8790 (t80) cc_final: 0.8444 (t80) REVERT: L 94 ASP cc_start: 0.6826 (t0) cc_final: 0.6532 (t0) REVERT: H 19 ARG cc_start: 0.7563 (ttm170) cc_final: 0.6782 (ttp80) REVERT: F 338 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7164 (p90) REVERT: F 386 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7789 (mttp) outliers start: 16 outliers final: 13 residues processed: 67 average time/residue: 0.1431 time to fit residues: 11.9144 Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.150211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.132502 restraints weight = 4640.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135802 restraints weight = 2525.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138016 restraints weight = 1691.495| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 3387 Z= 0.257 Angle : 0.672 8.092 4604 Z= 0.343 Chirality : 0.045 0.151 489 Planarity : 0.004 0.044 594 Dihedral : 6.253 45.068 516 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 4.83 % Allowed : 16.76 % Favored : 78.41 % 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: -3.29 (0.38), residues: 416 helix: -4.85 (0.35), residues: 20 sheet: -1.62 (0.43), residues: 146 loop : -2.38 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 353 HIS 0.004 0.002 HIS F 449 PHE 0.021 0.002 PHE F 338 TYR 0.015 0.002 TYR H 94 ARG 0.003 0.000 ARG F 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 1) link_NAG-ASN : angle 1.95472 ( 3) link_BETA1-4 : bond 0.00253 ( 1) link_BETA1-4 : angle 0.94406 ( 3) hydrogen bonds : bond 0.03484 ( 69) hydrogen bonds : angle 6.12848 ( 159) SS BOND : bond 0.00521 ( 2) SS BOND : angle 1.26277 ( 4) covalent geometry : bond 0.00639 ( 3383) covalent geometry : angle 0.66926 ( 4594) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.360 Fit side-chains REVERT: L 93 TYR cc_start: 0.8803 (t80) cc_final: 0.8424 (t80) REVERT: L 94 ASP cc_start: 0.6853 (t0) cc_final: 0.6519 (t0) REVERT: H 19 ARG cc_start: 0.7572 (ttm170) cc_final: 0.6783 (ttp80) REVERT: H 98 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.6902 (ttt90) REVERT: F 338 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7468 (p90) REVERT: F 386 LYS cc_start: 0.8238 (tmtt) cc_final: 0.7802 (mttp) outliers start: 17 outliers final: 14 residues processed: 69 average time/residue: 0.1562 time to fit residues: 13.2058 Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 22 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.154919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137678 restraints weight = 4593.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140843 restraints weight = 2546.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143031 restraints weight = 1718.399| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3387 Z= 0.133 Angle : 0.577 6.762 4604 Z= 0.296 Chirality : 0.042 0.161 489 Planarity : 0.004 0.035 594 Dihedral : 5.721 42.648 516 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.69 % Allowed : 18.18 % Favored : 78.12 % 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: -3.03 (0.39), residues: 416 helix: -4.78 (0.39), residues: 20 sheet: -1.40 (0.44), residues: 146 loop : -2.22 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 353 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE H 53 TYR 0.014 0.001 TYR F 369 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 1) link_NAG-ASN : angle 1.23875 ( 3) link_BETA1-4 : bond 0.00405 ( 1) link_BETA1-4 : angle 0.85645 ( 3) hydrogen bonds : bond 0.02961 ( 69) hydrogen bonds : angle 6.06366 ( 159) SS BOND : bond 0.00221 ( 2) SS BOND : angle 1.12840 ( 4) covalent geometry : bond 0.00324 ( 3383) covalent geometry : angle 0.57511 ( 4594) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.360 Fit side-chains REVERT: L 93 TYR cc_start: 0.8694 (t80) cc_final: 0.8378 (t80) REVERT: L 94 ASP cc_start: 0.6828 (t0) cc_final: 0.6396 (t0) REVERT: H 19 ARG cc_start: 0.7468 (ttm170) cc_final: 0.6762 (ttp80) REVERT: H 94 TYR cc_start: 0.8134 (m-80) cc_final: 0.7374 (m-80) REVERT: F 338 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7169 (p90) REVERT: F 386 LYS cc_start: 0.8060 (tmtt) cc_final: 0.7767 (mmmt) REVERT: F 454 ARG cc_start: 0.8852 (tpp80) cc_final: 0.8501 (ttm-80) outliers start: 13 outliers final: 12 residues processed: 68 average time/residue: 0.1556 time to fit residues: 12.9737 Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 25 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.149678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132759 restraints weight = 4585.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135975 restraints weight = 2499.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138142 restraints weight = 1662.549| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3387 Z= 0.164 Angle : 0.596 7.677 4604 Z= 0.304 Chirality : 0.043 0.158 489 Planarity : 0.004 0.034 594 Dihedral : 5.661 41.171 516 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.69 % Allowed : 18.47 % Favored : 77.84 % 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 (0.39), residues: 416 helix: -4.84 (0.35), residues: 20 sheet: -1.40 (0.44), residues: 146 loop : -2.14 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 353 HIS 0.003 0.002 HIS H 35 PHE 0.015 0.001 PHE H 53 TYR 0.014 0.001 TYR F 369 ARG 0.006 0.001 ARG H 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 1) link_NAG-ASN : angle 1.44922 ( 3) link_BETA1-4 : bond 0.00438 ( 1) link_BETA1-4 : angle 0.90400 ( 3) hydrogen bonds : bond 0.03067 ( 69) hydrogen bonds : angle 5.91541 ( 159) SS BOND : bond 0.00291 ( 2) SS BOND : angle 1.15624 ( 4) covalent geometry : bond 0.00406 ( 3383) covalent geometry : angle 0.59454 ( 4594) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.365 Fit side-chains REVERT: L 93 TYR cc_start: 0.8744 (t80) cc_final: 0.8489 (t80) REVERT: H 19 ARG cc_start: 0.7476 (ttm170) cc_final: 0.6765 (ttp80) REVERT: H 94 TYR cc_start: 0.8199 (m-80) cc_final: 0.7446 (m-80) REVERT: F 338 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7184 (p90) REVERT: F 386 LYS cc_start: 0.8096 (tmtt) cc_final: 0.7771 (mmmt) REVERT: F 454 ARG cc_start: 0.8883 (tpp80) cc_final: 0.8414 (ttm-80) outliers start: 13 outliers final: 11 residues processed: 65 average time/residue: 0.1342 time to fit residues: 11.0410 Evaluate side-chains 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.421 > 50: distance: 7 - 9: 23.726 distance: 9 - 10: 23.439 distance: 10 - 11: 29.136 distance: 11 - 12: 30.561 distance: 11 - 13: 34.275 distance: 12 - 148: 18.007 distance: 13 - 14: 38.130 distance: 14 - 15: 32.083 distance: 14 - 17: 7.167 distance: 15 - 16: 26.139 distance: 15 - 20: 25.685 distance: 17 - 18: 22.513 distance: 17 - 19: 13.087 distance: 20 - 21: 19.760 distance: 20 - 151: 26.120 distance: 21 - 22: 12.641 distance: 21 - 24: 12.020 distance: 22 - 23: 25.019 distance: 22 - 27: 21.119 distance: 24 - 25: 16.118 distance: 24 - 26: 20.406 distance: 27 - 28: 19.895 distance: 28 - 29: 24.978 distance: 28 - 31: 15.280 distance: 29 - 30: 14.432 distance: 29 - 36: 24.056 distance: 31 - 32: 13.352 distance: 32 - 33: 18.769 distance: 33 - 34: 22.276 distance: 33 - 35: 8.143 distance: 36 - 37: 20.952 distance: 36 - 42: 32.197 distance: 37 - 38: 29.230 distance: 37 - 40: 12.322 distance: 38 - 39: 16.681 distance: 38 - 43: 34.830 distance: 40 - 41: 19.800 distance: 41 - 42: 20.321 distance: 43 - 44: 30.245 distance: 44 - 45: 17.687 distance: 45 - 46: 17.625 distance: 45 - 47: 25.004 distance: 47 - 48: 27.157 distance: 48 - 49: 26.644 distance: 48 - 51: 13.292 distance: 49 - 50: 9.149 distance: 49 - 58: 43.219 distance: 51 - 52: 10.545 distance: 52 - 53: 14.318 distance: 53 - 54: 7.143 distance: 54 - 55: 5.602 distance: 55 - 56: 4.916 distance: 55 - 57: 5.309 distance: 58 - 59: 23.119 distance: 59 - 60: 8.081 distance: 59 - 62: 7.362 distance: 60 - 61: 17.712 distance: 60 - 64: 4.166 distance: 62 - 63: 21.583 distance: 64 - 65: 6.482 distance: 64 - 111: 11.813 distance: 65 - 66: 8.618 distance: 65 - 68: 7.247 distance: 66 - 67: 10.664 distance: 67 - 108: 13.773 distance: 68 - 69: 6.524 distance: 69 - 71: 8.539 distance: 72 - 73: 3.251 distance: 74 - 83: 3.771