Starting phenix.real_space_refine on Wed Jun 4 15:40:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7won_32652/06_2025/7won_32652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7won_32652/06_2025/7won_32652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7won_32652/06_2025/7won_32652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7won_32652/06_2025/7won_32652.map" model { file = "/net/cci-nas-00/data/ceres_data/7won_32652/06_2025/7won_32652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7won_32652/06_2025/7won_32652.cif" } resolution = 3.9 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= 0.010 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 15 5.16 5 C 2098 2.51 5 N 556 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3318 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 811 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} 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: "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: 5.61, per 1000 atoms: 1.69 Number of scatterers: 3318 At special positions: 0 Unit cell: (73.132, 84.024, 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 15 16.00 O 649 8.00 N 556 7.00 C 2098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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: 0.84 Conformation dependent library (CDL) restraints added in 398.6 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 8 sheets defined 1.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.532A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 356 through 358 removed outlier: 3.564A pdb=" N LYS F 356 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.501A pdb=" N SER L 69 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.712A 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 51 removed outlier: 5.896A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.748A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.113A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 102 through 104 66 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 538 1.30 - 1.43: 1004 1.43 - 1.56: 1840 1.56 - 1.69: 0 1.69 - 1.82: 19 Bond restraints: 3401 Sorted by residual: bond pdb=" C ARG H 106 " pdb=" N SER H 107 " ideal model delta sigma weight residual 1.332 1.240 0.092 1.40e-02 5.10e+03 4.33e+01 bond pdb=" C ARG H 106 " pdb=" O ARG H 106 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.16e-02 7.43e+03 3.19e+01 bond pdb=" CA ASP H 113 " pdb=" C ASP H 113 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.28e-02 6.10e+03 2.98e+01 bond pdb=" CA ARG H 106 " pdb=" C ARG H 106 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.26e-02 6.30e+03 1.35e+01 bond pdb=" CA ARG H 106 " pdb=" CB ARG H 106 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.58e-02 4.01e+03 1.27e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 4523 2.84 - 5.69: 80 5.69 - 8.53: 12 8.53 - 11.37: 2 11.37 - 14.22: 3 Bond angle restraints: 4620 Sorted by residual: angle pdb=" N TYR H 103 " pdb=" CA TYR H 103 " pdb=" C TYR H 103 " ideal model delta sigma weight residual 109.52 121.19 -11.67 1.55e+00 4.16e-01 5.67e+01 angle pdb=" O VAL H 100 " pdb=" C VAL H 100 " pdb=" N GLN H 101 " ideal model delta sigma weight residual 122.57 114.38 8.19 1.25e+00 6.40e-01 4.30e+01 angle pdb=" N LEU H 112 " pdb=" CA LEU H 112 " pdb=" C LEU H 112 " ideal model delta sigma weight residual 110.35 101.53 8.82 1.36e+00 5.41e-01 4.21e+01 angle pdb=" C ARG H 106 " pdb=" N SER H 107 " pdb=" CA SER H 107 " ideal model delta sigma weight residual 121.54 109.28 12.26 1.91e+00 2.74e-01 4.12e+01 angle pdb=" CA ARG H 106 " pdb=" C ARG H 106 " pdb=" O ARG H 106 " ideal model delta sigma weight residual 120.70 127.27 -6.57 1.03e+00 9.43e-01 4.06e+01 ... (remaining 4615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.55: 1823 20.55 - 41.09: 143 41.09 - 61.64: 19 61.64 - 82.18: 6 82.18 - 102.73: 10 Dihedral angle restraints: 2001 sinusoidal: 787 harmonic: 1214 Sorted by residual: dihedral pdb=" CA PHE F 429 " pdb=" C PHE F 429 " pdb=" N THR F 430 " pdb=" CA THR F 430 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASN F 460 " pdb=" C ASN F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA CYS F 336 " pdb=" C CYS F 336 " pdb=" N PRO F 337 " pdb=" CA PRO F 337 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 365 0.059 - 0.119: 101 0.119 - 0.178: 19 0.178 - 0.238: 6 0.238 - 0.297: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ASP H 113 " pdb=" N ASP H 113 " pdb=" C ASP H 113 " pdb=" CB ASP H 113 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA TYR H 103 " pdb=" N TYR H 103 " pdb=" C TYR H 103 " pdb=" CB TYR H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 489 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 100 " 0.042 2.00e-02 2.50e+03 7.95e-02 6.33e+01 pdb=" C VAL H 100 " -0.138 2.00e-02 2.50e+03 pdb=" O VAL H 100 " 0.051 2.00e-02 2.50e+03 pdb=" N GLN H 101 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 462 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO F 463 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 463 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 463 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 56 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO L 57 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 57 " 0.033 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 50 2.61 - 3.18: 2613 3.18 - 3.75: 4748 3.75 - 4.33: 6402 4.33 - 4.90: 10870 Nonbonded interactions: 24683 Sorted by model distance: nonbonded pdb=" O ARG H 106 " pdb=" C SER H 107 " model vdw 2.035 3.270 nonbonded pdb=" O SER F 371 " pdb=" NH1 ARG H 106 " model vdw 2.238 3.120 nonbonded pdb=" O ASN F 439 " pdb=" OG SER F 443 " model vdw 2.276 3.040 nonbonded pdb=" O ARG H 106 " pdb=" CA SER H 107 " model vdw 2.278 2.776 nonbonded pdb=" OG SER F 349 " pdb=" O LEU F 452 " model vdw 2.302 3.040 ... (remaining 24678 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: 11.710 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: 0.050 Process input model: 15.510 Find NCS groups from input model: 0.030 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 : 0.006 0.092 3406 Z= 0.359 Angle : 0.978 14.217 4632 Z= 0.563 Chirality : 0.060 0.297 492 Planarity : 0.008 0.080 600 Dihedral : 16.809 102.726 1232 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.28 % Allowed : 10.14 % Favored : 89.58 % 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: -4.42 (0.35), residues: 419 helix: -4.82 (0.44), residues: 14 sheet: -2.40 (0.44), residues: 127 loop : -3.30 (0.30), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 436 HIS 0.006 0.003 HIS H 35 PHE 0.011 0.002 PHE F 400 TYR 0.021 0.002 TYR H 104 ARG 0.007 0.001 ARG H 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 0.76846 ( 3) link_BETA1-4 : bond 0.01260 ( 1) link_BETA1-4 : angle 2.10600 ( 3) hydrogen bonds : bond 0.30355 ( 66) hydrogen bonds : angle 11.76116 ( 168) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.61938 ( 6) covalent geometry : bond 0.00604 ( 3401) covalent geometry : angle 0.97704 ( 4620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8755 (p0) cc_final: 0.8457 (p0) REVERT: F 474 GLN cc_start: 0.6126 (tp40) cc_final: 0.5872 (tm-30) REVERT: L 16 GLN cc_start: 0.8730 (mm110) cc_final: 0.8170 (mp10) REVERT: H 16 ARG cc_start: 0.2340 (mmt180) cc_final: 0.1977 (mmt180) outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1904 time to fit residues: 21.3211 Evaluate side-chains 78 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 106 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 370 ASN F 388 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN F 487 ASN L 6 GLN L 16 GLN L 40 GLN H 13 GLN H 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.109778 restraints weight = 5056.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111950 restraints weight = 3623.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113400 restraints weight = 2905.026| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3406 Z= 0.222 Angle : 0.699 8.421 4632 Z= 0.355 Chirality : 0.048 0.214 492 Planarity : 0.005 0.045 600 Dihedral : 12.083 78.853 522 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 4.79 % Allowed : 19.72 % Favored : 75.49 % 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: -4.02 (0.38), residues: 419 helix: -4.52 (0.76), residues: 14 sheet: -2.34 (0.44), residues: 132 loop : -2.88 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 436 HIS 0.003 0.001 HIS H 35 PHE 0.018 0.002 PHE F 338 TYR 0.017 0.002 TYR F 495 ARG 0.004 0.001 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 1) link_NAG-ASN : angle 0.67391 ( 3) link_BETA1-4 : bond 0.00719 ( 1) link_BETA1-4 : angle 2.41143 ( 3) hydrogen bonds : bond 0.05669 ( 66) hydrogen bonds : angle 8.08524 ( 168) SS BOND : bond 0.00257 ( 3) SS BOND : angle 0.56362 ( 6) covalent geometry : bond 0.00509 ( 3401) covalent geometry : angle 0.69629 ( 4620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.335 Fit side-chains REVERT: F 346 ARG cc_start: 0.7298 (tpp-160) cc_final: 0.7093 (tpp80) REVERT: F 354 ASN cc_start: 0.8886 (p0) cc_final: 0.8562 (p0) REVERT: F 427 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7962 (t0) REVERT: F 474 GLN cc_start: 0.6092 (tp40) cc_final: 0.5767 (tm-30) REVERT: L 6 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8769 (pt0) REVERT: L 16 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8098 (mp10) REVERT: H 16 ARG cc_start: 0.2304 (mmt180) cc_final: 0.1996 (mmt180) outliers start: 17 outliers final: 10 residues processed: 98 average time/residue: 0.1950 time to fit residues: 22.3098 Evaluate side-chains 92 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN L 6 GLN L 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115294 restraints weight = 4928.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118044 restraints weight = 3290.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.119994 restraints weight = 2498.342| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3406 Z= 0.150 Angle : 0.659 9.737 4632 Z= 0.325 Chirality : 0.046 0.244 492 Planarity : 0.004 0.038 600 Dihedral : 10.322 66.025 518 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 3.38 % Allowed : 20.85 % Favored : 75.77 % 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: -3.63 (0.39), residues: 419 helix: -4.60 (0.68), residues: 14 sheet: -2.04 (0.45), residues: 133 loop : -2.60 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 436 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE F 338 TYR 0.014 0.001 TYR F 369 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 0.53534 ( 3) link_BETA1-4 : bond 0.00918 ( 1) link_BETA1-4 : angle 2.70439 ( 3) hydrogen bonds : bond 0.04438 ( 66) hydrogen bonds : angle 7.26079 ( 168) SS BOND : bond 0.00203 ( 3) SS BOND : angle 0.63483 ( 6) covalent geometry : bond 0.00346 ( 3401) covalent geometry : angle 0.65522 ( 4620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8860 (p0) cc_final: 0.8500 (p0) REVERT: F 474 GLN cc_start: 0.5912 (tp40) cc_final: 0.5372 (tm-30) REVERT: L 16 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8121 (mp10) REVERT: H 16 ARG cc_start: 0.2433 (mmt180) cc_final: 0.0200 (mmt180) REVERT: H 113 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8495 (m-30) outliers start: 12 outliers final: 8 residues processed: 90 average time/residue: 0.2053 time to fit residues: 21.4337 Evaluate side-chains 87 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 7 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113600 restraints weight = 5068.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116411 restraints weight = 3378.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.118322 restraints weight = 2561.804| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3406 Z= 0.170 Angle : 0.662 9.763 4632 Z= 0.324 Chirality : 0.047 0.232 492 Planarity : 0.004 0.033 600 Dihedral : 9.128 56.245 518 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 5.07 % Allowed : 19.44 % Favored : 75.49 % 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: -3.50 (0.40), residues: 419 helix: -4.53 (0.72), residues: 14 sheet: -1.95 (0.46), residues: 133 loop : -2.51 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 436 HIS 0.004 0.002 HIS H 35 PHE 0.013 0.002 PHE F 338 TYR 0.024 0.002 TYR H 114 ARG 0.003 0.000 ARG F 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 1) link_NAG-ASN : angle 0.69948 ( 3) link_BETA1-4 : bond 0.01200 ( 1) link_BETA1-4 : angle 3.09602 ( 3) hydrogen bonds : bond 0.04134 ( 66) hydrogen bonds : angle 6.75495 ( 168) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.65206 ( 6) covalent geometry : bond 0.00395 ( 3401) covalent geometry : angle 0.65724 ( 4620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.360 Fit side-chains REVERT: F 354 ASN cc_start: 0.8896 (p0) cc_final: 0.8577 (p0) REVERT: F 474 GLN cc_start: 0.5972 (tp40) cc_final: 0.5349 (tm-30) REVERT: L 16 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8125 (mp10) REVERT: H 16 ARG cc_start: 0.2269 (mmt180) cc_final: 0.1916 (mmt180) REVERT: H 113 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8490 (m-30) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 0.1764 time to fit residues: 19.0446 Evaluate side-chains 87 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 0.0040 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.137070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115216 restraints weight = 4996.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117958 restraints weight = 3315.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119931 restraints weight = 2523.218| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3406 Z= 0.133 Angle : 0.642 9.451 4632 Z= 0.312 Chirality : 0.046 0.214 492 Planarity : 0.004 0.034 600 Dihedral : 8.156 57.518 518 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 4.51 % Allowed : 20.85 % Favored : 74.65 % 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: -3.31 (0.40), residues: 419 helix: -4.56 (0.74), residues: 14 sheet: -1.82 (0.46), residues: 133 loop : -2.37 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.011 0.001 PHE F 429 TYR 0.025 0.001 TYR H 114 ARG 0.005 0.001 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 1) link_NAG-ASN : angle 1.07826 ( 3) link_BETA1-4 : bond 0.01138 ( 1) link_BETA1-4 : angle 3.10410 ( 3) hydrogen bonds : bond 0.03584 ( 66) hydrogen bonds : angle 6.46999 ( 168) SS BOND : bond 0.00194 ( 3) SS BOND : angle 0.61648 ( 6) covalent geometry : bond 0.00304 ( 3401) covalent geometry : angle 0.63747 ( 4620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.377 Fit side-chains REVERT: F 354 ASN cc_start: 0.8843 (p0) cc_final: 0.8490 (p0) REVERT: F 474 GLN cc_start: 0.5940 (tp40) cc_final: 0.5394 (tm-30) REVERT: L 16 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8152 (mp10) REVERT: H 16 ARG cc_start: 0.2650 (mmt180) cc_final: 0.0368 (mmt180) REVERT: H 25 SER cc_start: 0.9330 (t) cc_final: 0.9019 (m) REVERT: H 53 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7063 (t80) REVERT: H 113 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8507 (m-30) outliers start: 16 outliers final: 11 residues processed: 92 average time/residue: 0.1881 time to fit residues: 20.5077 Evaluate side-chains 89 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.109638 restraints weight = 5114.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.112425 restraints weight = 3383.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114382 restraints weight = 2554.529| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3406 Z= 0.181 Angle : 0.670 9.361 4632 Z= 0.328 Chirality : 0.047 0.222 492 Planarity : 0.004 0.032 600 Dihedral : 8.005 59.380 518 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 4.23 % Allowed : 22.54 % Favored : 73.24 % 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: -3.26 (0.40), residues: 419 helix: -4.94 (0.42), residues: 20 sheet: -1.75 (0.47), residues: 127 loop : -2.25 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.012 0.002 PHE F 338 TYR 0.022 0.002 TYR H 114 ARG 0.003 0.000 ARG F 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 1.14292 ( 3) link_BETA1-4 : bond 0.01205 ( 1) link_BETA1-4 : angle 3.19911 ( 3) hydrogen bonds : bond 0.03874 ( 66) hydrogen bonds : angle 6.35976 ( 168) SS BOND : bond 0.00214 ( 3) SS BOND : angle 0.70292 ( 6) covalent geometry : bond 0.00422 ( 3401) covalent geometry : angle 0.66501 ( 4620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.335 Fit side-chains REVERT: F 354 ASN cc_start: 0.8876 (p0) cc_final: 0.8517 (p0) REVERT: F 474 GLN cc_start: 0.6027 (tp40) cc_final: 0.5385 (tm-30) REVERT: L 16 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8115 (mp10) REVERT: H 16 ARG cc_start: 0.2395 (mmt180) cc_final: 0.1990 (mmt180) REVERT: H 53 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7265 (t80) outliers start: 15 outliers final: 12 residues processed: 87 average time/residue: 0.1895 time to fit residues: 19.5082 Evaluate side-chains 90 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109172 restraints weight = 5006.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111776 restraints weight = 3331.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113702 restraints weight = 2558.357| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3406 Z= 0.183 Angle : 0.670 9.628 4632 Z= 0.329 Chirality : 0.047 0.230 492 Planarity : 0.004 0.032 600 Dihedral : 7.763 59.470 518 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 4.51 % Allowed : 22.54 % Favored : 72.96 % 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: -3.21 (0.40), residues: 419 helix: -4.91 (0.39), residues: 20 sheet: -1.71 (0.48), residues: 127 loop : -2.21 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 436 HIS 0.004 0.002 HIS H 35 PHE 0.014 0.002 PHE F 429 TYR 0.030 0.002 TYR H 114 ARG 0.006 0.001 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00003 ( 1) link_NAG-ASN : angle 1.26253 ( 3) link_BETA1-4 : bond 0.01176 ( 1) link_BETA1-4 : angle 3.17218 ( 3) hydrogen bonds : bond 0.03765 ( 66) hydrogen bonds : angle 6.29554 ( 168) SS BOND : bond 0.00248 ( 3) SS BOND : angle 0.71289 ( 6) covalent geometry : bond 0.00425 ( 3401) covalent geometry : angle 0.66462 ( 4620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.368 Fit side-chains REVERT: F 354 ASN cc_start: 0.8873 (p0) cc_final: 0.8514 (p0) REVERT: F 474 GLN cc_start: 0.5975 (tp40) cc_final: 0.5373 (tm-30) REVERT: L 16 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8107 (mp10) REVERT: H 16 ARG cc_start: 0.2257 (mmt180) cc_final: 0.1849 (mmt180) REVERT: H 113 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8420 (m-30) outliers start: 16 outliers final: 13 residues processed: 90 average time/residue: 0.1843 time to fit residues: 19.4870 Evaluate side-chains 89 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.113108 restraints weight = 4991.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.115817 restraints weight = 3332.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117536 restraints weight = 2540.716| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3406 Z= 0.169 Angle : 0.680 10.199 4632 Z= 0.327 Chirality : 0.046 0.235 492 Planarity : 0.004 0.032 600 Dihedral : 7.534 58.780 518 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 5.35 % Allowed : 22.25 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.40), residues: 419 helix: -4.90 (0.39), residues: 20 sheet: -1.60 (0.48), residues: 127 loop : -2.15 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 436 HIS 0.004 0.002 HIS H 35 PHE 0.012 0.002 PHE F 338 TYR 0.026 0.002 TYR H 114 ARG 0.007 0.001 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00029 ( 1) link_NAG-ASN : angle 1.31691 ( 3) link_BETA1-4 : bond 0.01134 ( 1) link_BETA1-4 : angle 3.12011 ( 3) hydrogen bonds : bond 0.03648 ( 66) hydrogen bonds : angle 6.24160 ( 168) SS BOND : bond 0.00121 ( 3) SS BOND : angle 1.45260 ( 6) covalent geometry : bond 0.00395 ( 3401) covalent geometry : angle 0.67293 ( 4620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.345 Fit side-chains REVERT: F 354 ASN cc_start: 0.8855 (p0) cc_final: 0.8509 (p0) REVERT: F 474 GLN cc_start: 0.6005 (tp40) cc_final: 0.5352 (tm-30) REVERT: L 16 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8087 (mp10) REVERT: L 93 TYR cc_start: 0.8083 (t80) cc_final: 0.7574 (t80) REVERT: H 16 ARG cc_start: 0.2349 (mmt180) cc_final: 0.1943 (mmt180) REVERT: H 113 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8392 (m-30) REVERT: H 118 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8386 (mtt) outliers start: 19 outliers final: 14 residues processed: 89 average time/residue: 0.1762 time to fit residues: 18.8087 Evaluate side-chains 91 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 3 optimal weight: 0.5980 chunk 35 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.135375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113689 restraints weight = 4998.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116439 restraints weight = 3306.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118371 restraints weight = 2501.858| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3406 Z= 0.154 Angle : 0.667 10.281 4632 Z= 0.320 Chirality : 0.046 0.241 492 Planarity : 0.004 0.032 600 Dihedral : 7.208 56.271 518 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 4.51 % Allowed : 23.38 % Favored : 72.11 % 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: -3.01 (0.41), residues: 419 helix: -4.84 (0.41), residues: 20 sheet: -1.46 (0.49), residues: 128 loop : -2.13 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.010 0.002 PHE F 338 TYR 0.027 0.002 TYR H 114 ARG 0.006 0.001 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 1) link_NAG-ASN : angle 1.39870 ( 3) link_BETA1-4 : bond 0.01187 ( 1) link_BETA1-4 : angle 3.08439 ( 3) hydrogen bonds : bond 0.03363 ( 66) hydrogen bonds : angle 6.17218 ( 168) SS BOND : bond 0.00185 ( 3) SS BOND : angle 1.36493 ( 6) covalent geometry : bond 0.00360 ( 3401) covalent geometry : angle 0.66041 ( 4620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.336 Fit side-chains REVERT: F 354 ASN cc_start: 0.8815 (p0) cc_final: 0.8448 (p0) REVERT: F 474 GLN cc_start: 0.5876 (tp40) cc_final: 0.5330 (tm-30) REVERT: L 16 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8086 (mp10) REVERT: L 93 TYR cc_start: 0.7983 (t80) cc_final: 0.7714 (t80) REVERT: H 16 ARG cc_start: 0.2457 (mmt180) cc_final: 0.2051 (mmt180) REVERT: H 113 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8366 (m-30) REVERT: H 118 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8283 (mtt) outliers start: 16 outliers final: 14 residues processed: 89 average time/residue: 0.1982 time to fit residues: 20.8093 Evaluate side-chains 90 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.3980 chunk 35 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 16 optimal weight: 0.0040 overall best weight: 0.1948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116055 restraints weight = 4930.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118983 restraints weight = 3212.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121005 restraints weight = 2413.500| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3406 Z= 0.110 Angle : 0.646 9.975 4632 Z= 0.310 Chirality : 0.045 0.242 492 Planarity : 0.004 0.032 600 Dihedral : 6.438 50.023 518 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.66 % Allowed : 25.63 % Favored : 70.70 % 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: -2.80 (0.41), residues: 419 helix: -4.78 (0.44), residues: 20 sheet: -1.22 (0.49), residues: 126 loop : -2.03 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.010 0.001 PHE F 456 TYR 0.023 0.001 TYR H 114 ARG 0.006 0.000 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 1) link_NAG-ASN : angle 1.57873 ( 3) link_BETA1-4 : bond 0.01167 ( 1) link_BETA1-4 : angle 3.02163 ( 3) hydrogen bonds : bond 0.03000 ( 66) hydrogen bonds : angle 6.06006 ( 168) SS BOND : bond 0.00172 ( 3) SS BOND : angle 1.13508 ( 6) covalent geometry : bond 0.00250 ( 3401) covalent geometry : angle 0.63988 ( 4620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.359 Fit side-chains REVERT: F 354 ASN cc_start: 0.8794 (p0) cc_final: 0.8431 (p0) REVERT: F 474 GLN cc_start: 0.5928 (tp40) cc_final: 0.5410 (tm-30) REVERT: L 16 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8043 (mp10) REVERT: H 16 ARG cc_start: 0.2483 (mmt180) cc_final: -0.0537 (mpt180) REVERT: H 25 SER cc_start: 0.9323 (t) cc_final: 0.9015 (m) REVERT: H 113 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8365 (m-30) REVERT: H 118 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8002 (mtt) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1688 time to fit residues: 19.5183 Evaluate side-chains 98 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.135897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114365 restraints weight = 5041.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117039 restraints weight = 3268.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.119042 restraints weight = 2465.275| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3406 Z= 0.177 Angle : 0.697 9.339 4632 Z= 0.340 Chirality : 0.048 0.245 492 Planarity : 0.004 0.035 600 Dihedral : 6.637 49.667 518 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.10 % Allowed : 27.89 % Favored : 69.01 % 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: -2.81 (0.41), residues: 419 helix: -4.90 (0.64), residues: 14 sheet: -1.37 (0.48), residues: 126 loop : -2.03 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 436 HIS 0.006 0.002 HIS H 35 PHE 0.038 0.002 PHE H 29 TYR 0.033 0.002 TYR H 114 ARG 0.006 0.001 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 1) link_NAG-ASN : angle 1.48610 ( 3) link_BETA1-4 : bond 0.01119 ( 1) link_BETA1-4 : angle 3.03108 ( 3) hydrogen bonds : bond 0.03531 ( 66) hydrogen bonds : angle 6.10238 ( 168) SS BOND : bond 0.00295 ( 3) SS BOND : angle 1.35134 ( 6) covalent geometry : bond 0.00415 ( 3401) covalent geometry : angle 0.69039 ( 4620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2043.01 seconds wall clock time: 36 minutes 3.91 seconds (2163.91 seconds total)