Starting phenix.real_space_refine on Wed Jul 23 13:31:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wp1_32666/07_2025/7wp1_32666.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp1_32666/07_2025/7wp1_32666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wp1_32666/07_2025/7wp1_32666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp1_32666/07_2025/7wp1_32666.map" model { file = "/net/cci-nas-00/data/ceres_data/7wp1_32666/07_2025/7wp1_32666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp1_32666/07_2025/7wp1_32666.cif" } resolution = 3.77 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= 0.009 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 2096 2.51 5 N 551 2.21 5 O 643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3305 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: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1464 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, '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: 6.14, per 1000 atoms: 1.86 Number of scatterers: 3305 At special positions: 0 Unit cell: (87.914, 63.018, 81.69, 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 643 8.00 N 551 7.00 C 2096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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 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: 0.75 Conformation dependent library (CDL) restraints added in 373.6 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 7 sheets defined 4.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.536A pdb=" N GLY L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.853A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 410 removed outlier: 4.734A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.941A pdb=" N THR L 109 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY L 12 " --> 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 47 through 50 removed outlier: 6.500A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.636A pdb=" N THR H 125 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR H 94 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 92 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 376 through 378 removed outlier: 3.575A pdb=" N THR F 376 " --> pdb=" O ALA F 435 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 435 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 452 through 454 57 hydrogen bonds defined for protein. 123 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: 0.72 Time building geometry restraints manager: 0.90 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: 1021 1.34 - 1.46: 851 1.46 - 1.58: 1498 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3389 Sorted by residual: bond pdb=" CB ASN F 370 " pdb=" CG ASN F 370 " ideal model delta sigma weight residual 1.516 1.575 -0.059 2.50e-02 1.60e+03 5.61e+00 bond pdb=" CA ASN F 370 " pdb=" CB ASN F 370 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.43e-02 4.89e+03 5.60e+00 bond pdb=" C LEU F 425 " pdb=" N PRO F 426 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.25e-02 6.40e+03 3.51e+00 bond pdb=" C GLY L 12 " pdb=" N ALA L 13 " ideal model delta sigma weight residual 1.330 1.304 0.026 1.47e-02 4.63e+03 3.23e+00 bond pdb=" CA CYS F 336 " pdb=" C CYS F 336 " ideal model delta sigma weight residual 1.525 1.562 -0.037 2.10e-02 2.27e+03 3.10e+00 ... (remaining 3384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 4396 2.47 - 4.94: 170 4.94 - 7.41: 30 7.41 - 9.88: 6 9.88 - 12.34: 1 Bond angle restraints: 4603 Sorted by residual: angle pdb=" N VAL F 367 " pdb=" CA VAL F 367 " pdb=" C VAL F 367 " ideal model delta sigma weight residual 113.47 107.26 6.21 1.01e+00 9.80e-01 3.78e+01 angle pdb=" N ILE F 468 " pdb=" CA ILE F 468 " pdb=" C ILE F 468 " ideal model delta sigma weight residual 112.12 107.84 4.28 8.40e-01 1.42e+00 2.60e+01 angle pdb=" CA ASN F 370 " pdb=" CB ASN F 370 " pdb=" CG ASN F 370 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" N CYS F 391 " pdb=" CA CYS F 391 " pdb=" C CYS F 391 " ideal model delta sigma weight residual 113.23 118.58 -5.35 1.22e+00 6.72e-01 1.92e+01 angle pdb=" N TYR F 473 " pdb=" CA TYR F 473 " pdb=" C TYR F 473 " ideal model delta sigma weight residual 111.69 116.53 -4.84 1.23e+00 6.61e-01 1.55e+01 ... (remaining 4598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 1758 17.43 - 34.86: 196 34.86 - 52.29: 32 52.29 - 69.72: 4 69.72 - 87.15: 2 Dihedral angle restraints: 1992 sinusoidal: 783 harmonic: 1209 Sorted by residual: dihedral pdb=" CA LEU F 390 " pdb=" C LEU F 390 " pdb=" N CYS F 391 " pdb=" CA CYS F 391 " ideal model delta harmonic sigma weight residual 180.00 145.06 34.94 0 5.00e+00 4.00e-02 4.88e+01 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 -146.69 -33.31 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CA TYR F 380 " pdb=" C TYR F 380 " pdb=" N GLY F 381 " pdb=" CA GLY F 381 " ideal model delta harmonic sigma weight residual 180.00 -148.09 -31.91 0 5.00e+00 4.00e-02 4.07e+01 ... (remaining 1989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 474 0.138 - 0.277: 15 0.277 - 0.415: 0 0.415 - 0.553: 0 0.553 - 0.691: 1 Chirality restraints: 490 Sorted by residual: 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 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.18e+01 chirality pdb=" CA ASN F 370 " pdb=" N ASN F 370 " pdb=" C ASN F 370 " pdb=" CB ASN F 370 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 487 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.284 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" C7 NAG A 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.421 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.274 2.00e-02 2.50e+03 2.28e-01 6.52e+02 pdb=" C7 NAG A 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.384 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO H 14 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.036 5.00e-02 4.00e+02 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1171 2.85 - 3.36: 2769 3.36 - 3.88: 5198 3.88 - 4.39: 5643 4.39 - 4.90: 10286 Nonbonded interactions: 25067 Sorted by model distance: nonbonded pdb=" O SER F 366 " pdb=" OG SER F 366 " model vdw 2.338 3.040 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.345 3.040 nonbonded pdb=" NE2 HIS L 36 " pdb=" O ASN H 115 " model vdw 2.360 3.120 nonbonded pdb=" OG1 THR F 393 " pdb=" O GLU F 516 " model vdw 2.364 3.040 nonbonded pdb=" OH TYR L 38 " pdb=" OE1 GLN L 91 " model vdw 2.370 3.040 ... (remaining 25062 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: 9.530 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.090 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 0.059 3394 Z= 0.297 Angle : 1.181 12.344 4615 Z= 0.686 Chirality : 0.068 0.691 490 Planarity : 0.016 0.243 595 Dihedral : 14.456 87.147 1227 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.23 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 15.01 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -5.40 (0.31), residues: 417 helix: -5.32 (0.22), residues: 20 sheet: -3.25 (0.37), residues: 145 loop : -3.79 (0.28), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 436 HIS 0.006 0.003 HIS L 36 PHE 0.021 0.002 PHE F 338 TYR 0.018 0.002 TYR H 104 ARG 0.004 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.03583 ( 1) link_NAG-ASN : angle 5.53440 ( 3) link_BETA1-4 : bond 0.00371 ( 1) link_BETA1-4 : angle 3.81629 ( 3) hydrogen bonds : bond 0.27535 ( 57) hydrogen bonds : angle 10.86817 ( 123) SS BOND : bond 0.00338 ( 3) SS BOND : angle 0.79268 ( 6) covalent geometry : bond 0.00583 ( 3389) covalent geometry : angle 1.16953 ( 4603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.378 Fit side-chains REVERT: H 18 LEU cc_start: 0.6969 (tp) cc_final: 0.6738 (tp) REVERT: H 67 ARG cc_start: 0.7096 (mpt-90) cc_final: 0.6689 (mpt-90) REVERT: F 457 ARG cc_start: 0.8434 (ttt-90) cc_final: 0.7902 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2742 time to fit residues: 27.1032 Evaluate side-chains 67 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 37 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 39 GLN H 74 ASN F 388 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.153010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136527 restraints weight = 5253.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139849 restraints weight = 3197.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142219 restraints weight = 2200.255| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3394 Z= 0.210 Angle : 0.774 7.487 4615 Z= 0.408 Chirality : 0.051 0.301 490 Planarity : 0.006 0.053 595 Dihedral : 8.003 51.618 516 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.95 % Favored : 86.81 % Rotamer: Outliers : 4.53 % Allowed : 17.56 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.74 (0.34), residues: 417 helix: -5.28 (0.23), residues: 20 sheet: -2.74 (0.35), residues: 166 loop : -3.31 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 353 HIS 0.004 0.003 HIS L 36 PHE 0.018 0.002 PHE F 338 TYR 0.012 0.002 TYR F 421 ARG 0.006 0.001 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00808 ( 1) link_NAG-ASN : angle 3.68348 ( 3) link_BETA1-4 : bond 0.00226 ( 1) link_BETA1-4 : angle 2.63998 ( 3) hydrogen bonds : bond 0.03971 ( 57) hydrogen bonds : angle 7.64105 ( 123) SS BOND : bond 0.00360 ( 3) SS BOND : angle 0.78633 ( 6) covalent geometry : bond 0.00471 ( 3389) covalent geometry : angle 0.76622 ( 4603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.743 Fit side-chains REVERT: L 17 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6441 (ttp-110) REVERT: L 38 TYR cc_start: 0.9345 (m-80) cc_final: 0.9108 (m-80) REVERT: H 3 GLN cc_start: 0.8378 (pt0) cc_final: 0.8134 (pt0) REVERT: H 67 ARG cc_start: 0.7219 (mpt-90) cc_final: 0.7004 (mtt-85) REVERT: F 457 ARG cc_start: 0.8494 (ttt-90) cc_final: 0.7928 (ttt-90) outliers start: 16 outliers final: 13 residues processed: 79 average time/residue: 0.3249 time to fit residues: 29.5777 Evaluate side-chains 81 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS H 115 ASN F 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131618 restraints weight = 5213.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134921 restraints weight = 3204.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137068 restraints weight = 2212.582| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3394 Z= 0.270 Angle : 0.816 8.247 4615 Z= 0.427 Chirality : 0.053 0.327 490 Planarity : 0.006 0.055 595 Dihedral : 8.005 51.715 516 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.63 % Favored : 85.13 % Rotamer: Outliers : 7.65 % Allowed : 17.56 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.39 (0.37), residues: 417 helix: -5.29 (0.23), residues: 20 sheet: -2.49 (0.38), residues: 166 loop : -3.06 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 353 HIS 0.005 0.003 HIS H 35 PHE 0.023 0.002 PHE F 338 TYR 0.025 0.002 TYR H 80 ARG 0.004 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 1) link_NAG-ASN : angle 3.73221 ( 3) link_BETA1-4 : bond 0.00110 ( 1) link_BETA1-4 : angle 3.08244 ( 3) hydrogen bonds : bond 0.03328 ( 57) hydrogen bonds : angle 7.19470 ( 123) SS BOND : bond 0.00494 ( 3) SS BOND : angle 0.89575 ( 6) covalent geometry : bond 0.00619 ( 3389) covalent geometry : angle 0.80728 ( 4603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 1.038 Fit side-chains REVERT: L 17 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6360 (ttp-110) REVERT: F 369 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7230 (t80) REVERT: F 457 ARG cc_start: 0.8485 (ttt-90) cc_final: 0.7813 (ttt-90) outliers start: 27 outliers final: 19 residues processed: 86 average time/residue: 0.2974 time to fit residues: 29.7041 Evaluate side-chains 86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.1980 chunk 28 optimal weight: 0.0070 chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 21 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 overall best weight: 0.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138150 restraints weight = 5286.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141645 restraints weight = 3148.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144022 restraints weight = 2122.705| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3394 Z= 0.129 Angle : 0.710 8.551 4615 Z= 0.366 Chirality : 0.048 0.307 490 Planarity : 0.005 0.049 595 Dihedral : 7.045 44.442 516 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.23 % Favored : 87.53 % Rotamer: Outliers : 5.95 % Allowed : 21.25 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.17 (0.38), residues: 417 helix: -5.20 (0.28), residues: 20 sheet: -2.42 (0.38), residues: 171 loop : -2.82 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 353 HIS 0.007 0.004 HIS L 36 PHE 0.012 0.001 PHE F 392 TYR 0.013 0.001 TYR H 80 ARG 0.006 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00990 ( 1) link_NAG-ASN : angle 3.98840 ( 3) link_BETA1-4 : bond 0.00065 ( 1) link_BETA1-4 : angle 2.60042 ( 3) hydrogen bonds : bond 0.02636 ( 57) hydrogen bonds : angle 6.54716 ( 123) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.65170 ( 6) covalent geometry : bond 0.00281 ( 3389) covalent geometry : angle 0.70004 ( 4603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: H 101 GLN cc_start: 0.7106 (tm-30) cc_final: 0.6790 (tm-30) REVERT: F 369 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.6974 (t80) REVERT: F 457 ARG cc_start: 0.8309 (ttt-90) cc_final: 0.7850 (ttt-90) outliers start: 21 outliers final: 17 residues processed: 85 average time/residue: 0.1946 time to fit residues: 19.4057 Evaluate side-chains 83 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 chunk 36 optimal weight: 0.8980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136783 restraints weight = 5256.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140017 restraints weight = 3198.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142173 restraints weight = 2200.314| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3394 Z= 0.159 Angle : 0.715 7.188 4615 Z= 0.368 Chirality : 0.049 0.306 490 Planarity : 0.005 0.049 595 Dihedral : 6.864 43.334 516 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.99 % Favored : 87.77 % Rotamer: Outliers : 5.38 % Allowed : 22.10 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.38), residues: 417 helix: -5.15 (0.29), residues: 20 sheet: -2.36 (0.38), residues: 171 loop : -2.69 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 353 HIS 0.006 0.003 HIS L 36 PHE 0.013 0.001 PHE F 392 TYR 0.024 0.002 TYR H 80 ARG 0.005 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00845 ( 1) link_NAG-ASN : angle 3.98524 ( 3) link_BETA1-4 : bond 0.00011 ( 1) link_BETA1-4 : angle 2.79144 ( 3) hydrogen bonds : bond 0.02642 ( 57) hydrogen bonds : angle 6.42234 ( 123) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.73914 ( 6) covalent geometry : bond 0.00361 ( 3389) covalent geometry : angle 0.70447 ( 4603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.373 Fit side-chains REVERT: H 101 GLN cc_start: 0.7252 (tm-30) cc_final: 0.6785 (tm-30) REVERT: F 369 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.7057 (t80) REVERT: F 457 ARG cc_start: 0.8281 (ttt-90) cc_final: 0.7819 (ttt-90) outliers start: 19 outliers final: 16 residues processed: 85 average time/residue: 0.2248 time to fit residues: 22.1969 Evaluate side-chains 87 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 16 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138511 restraints weight = 5299.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141963 restraints weight = 3134.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144347 restraints weight = 2110.608| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3394 Z= 0.133 Angle : 0.701 8.034 4615 Z= 0.358 Chirality : 0.048 0.303 490 Planarity : 0.005 0.054 595 Dihedral : 6.556 40.981 516 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.99 % Favored : 87.77 % Rotamer: Outliers : 6.52 % Allowed : 22.38 % Favored : 71.10 % 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: -3.91 (0.39), residues: 417 helix: -5.07 (0.34), residues: 19 sheet: -2.28 (0.39), residues: 172 loop : -2.62 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 353 HIS 0.006 0.003 HIS L 36 PHE 0.011 0.001 PHE F 392 TYR 0.029 0.001 TYR H 80 ARG 0.005 0.001 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00922 ( 1) link_NAG-ASN : angle 4.03795 ( 3) link_BETA1-4 : bond 0.00068 ( 1) link_BETA1-4 : angle 2.64590 ( 3) hydrogen bonds : bond 0.02466 ( 57) hydrogen bonds : angle 6.21289 ( 123) SS BOND : bond 0.00197 ( 3) SS BOND : angle 0.73296 ( 6) covalent geometry : bond 0.00296 ( 3389) covalent geometry : angle 0.69010 ( 4603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.340 Fit side-chains REVERT: L 38 TYR cc_start: 0.9269 (m-80) cc_final: 0.9064 (m-80) REVERT: H 101 GLN cc_start: 0.7042 (tm-30) cc_final: 0.6603 (tm-30) REVERT: F 369 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.6974 (t80) REVERT: F 457 ARG cc_start: 0.8269 (ttt-90) cc_final: 0.7834 (ttt-90) outliers start: 23 outliers final: 18 residues processed: 87 average time/residue: 0.2007 time to fit residues: 20.4572 Evaluate side-chains 89 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 16 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 7 optimal weight: 0.1980 chunk 1 optimal weight: 0.3980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139352 restraints weight = 5131.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.142809 restraints weight = 3035.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145203 restraints weight = 2052.633| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3394 Z= 0.132 Angle : 0.691 8.059 4615 Z= 0.354 Chirality : 0.048 0.299 490 Planarity : 0.004 0.048 595 Dihedral : 6.390 39.814 516 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.51 % Favored : 88.25 % Rotamer: Outliers : 5.95 % Allowed : 22.66 % Favored : 71.39 % 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: -3.80 (0.39), residues: 417 helix: -4.98 (0.38), residues: 19 sheet: -2.21 (0.39), residues: 172 loop : -2.55 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 353 HIS 0.005 0.003 HIS L 36 PHE 0.010 0.001 PHE F 392 TYR 0.011 0.001 TYR F 380 ARG 0.004 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00874 ( 1) link_NAG-ASN : angle 4.00124 ( 3) link_BETA1-4 : bond 0.00138 ( 1) link_BETA1-4 : angle 2.63668 ( 3) hydrogen bonds : bond 0.02536 ( 57) hydrogen bonds : angle 6.18538 ( 123) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.79282 ( 6) covalent geometry : bond 0.00297 ( 3389) covalent geometry : angle 0.68041 ( 4603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: H 101 GLN cc_start: 0.7035 (tm-30) cc_final: 0.6613 (tm-30) REVERT: F 369 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.7030 (t80) REVERT: F 457 ARG cc_start: 0.8296 (ttt-90) cc_final: 0.7810 (ttt-90) outliers start: 21 outliers final: 19 residues processed: 86 average time/residue: 0.2917 time to fit residues: 31.0254 Evaluate side-chains 92 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.0170 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.154776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.137880 restraints weight = 5154.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141297 restraints weight = 3071.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143558 restraints weight = 2089.825| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3394 Z= 0.152 Angle : 0.709 7.569 4615 Z= 0.364 Chirality : 0.048 0.299 490 Planarity : 0.004 0.048 595 Dihedral : 6.482 40.593 516 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.51 % Favored : 88.25 % Rotamer: Outliers : 6.52 % Allowed : 21.53 % Favored : 71.95 % 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: -3.71 (0.39), residues: 417 helix: -4.85 (0.47), residues: 19 sheet: -2.18 (0.40), residues: 172 loop : -2.46 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 353 HIS 0.005 0.003 HIS L 36 PHE 0.011 0.001 PHE F 392 TYR 0.012 0.001 TYR H 59 ARG 0.004 0.000 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00814 ( 1) link_NAG-ASN : angle 3.98205 ( 3) link_BETA1-4 : bond 0.00157 ( 1) link_BETA1-4 : angle 2.78594 ( 3) hydrogen bonds : bond 0.02499 ( 57) hydrogen bonds : angle 6.24530 ( 123) SS BOND : bond 0.00196 ( 3) SS BOND : angle 0.82736 ( 6) covalent geometry : bond 0.00347 ( 3389) covalent geometry : angle 0.69798 ( 4603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.739 Fit side-chains REVERT: H 101 GLN cc_start: 0.7072 (tm-30) cc_final: 0.6862 (tm-30) REVERT: F 369 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.7071 (t80) outliers start: 23 outliers final: 17 residues processed: 87 average time/residue: 0.2663 time to fit residues: 27.4384 Evaluate side-chains 89 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.155830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138761 restraints weight = 5208.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.142167 restraints weight = 3100.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144535 restraints weight = 2117.714| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3394 Z= 0.139 Angle : 0.696 7.667 4615 Z= 0.358 Chirality : 0.047 0.299 490 Planarity : 0.004 0.048 595 Dihedral : 6.392 39.688 516 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.03 % Favored : 88.73 % Rotamer: Outliers : 5.95 % Allowed : 22.10 % Favored : 71.95 % 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: -3.67 (0.40), residues: 417 helix: -4.69 (0.59), residues: 19 sheet: -2.18 (0.40), residues: 172 loop : -2.42 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 353 HIS 0.005 0.003 HIS L 36 PHE 0.010 0.001 PHE F 392 TYR 0.012 0.001 TYR F 380 ARG 0.003 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 1) link_NAG-ASN : angle 3.99669 ( 3) link_BETA1-4 : bond 0.00164 ( 1) link_BETA1-4 : angle 2.76868 ( 3) hydrogen bonds : bond 0.02445 ( 57) hydrogen bonds : angle 6.19475 ( 123) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.76289 ( 6) covalent geometry : bond 0.00318 ( 3389) covalent geometry : angle 0.68548 ( 4603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.362 Fit side-chains REVERT: H 101 GLN cc_start: 0.6973 (tm-30) cc_final: 0.6726 (tm-30) REVERT: F 369 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7171 (t80) outliers start: 21 outliers final: 19 residues processed: 84 average time/residue: 0.4167 time to fit residues: 43.5532 Evaluate side-chains 90 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 14 optimal weight: 0.7980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.153675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136680 restraints weight = 5156.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140057 restraints weight = 3101.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142382 restraints weight = 2121.671| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3394 Z= 0.169 Angle : 0.715 7.088 4615 Z= 0.367 Chirality : 0.049 0.302 490 Planarity : 0.004 0.048 595 Dihedral : 6.629 41.244 516 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.75 % Favored : 88.01 % Rotamer: Outliers : 5.67 % Allowed : 22.95 % Favored : 71.39 % 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: -3.61 (0.40), residues: 417 helix: -4.68 (0.61), residues: 19 sheet: -2.15 (0.40), residues: 170 loop : -2.37 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 353 HIS 0.004 0.002 HIS H 35 PHE 0.013 0.001 PHE F 338 TYR 0.011 0.001 TYR F 380 ARG 0.003 0.000 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00774 ( 1) link_NAG-ASN : angle 3.95712 ( 3) link_BETA1-4 : bond 0.00236 ( 1) link_BETA1-4 : angle 2.98583 ( 3) hydrogen bonds : bond 0.02583 ( 57) hydrogen bonds : angle 6.38545 ( 123) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.80186 ( 6) covalent geometry : bond 0.00389 ( 3389) covalent geometry : angle 0.70366 ( 4603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 101 GLN cc_start: 0.7084 (tm-30) cc_final: 0.6853 (tm-30) REVERT: F 353 TRP cc_start: 0.7563 (p90) cc_final: 0.6906 (p90) REVERT: F 369 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7271 (t80) REVERT: F 440 ASN cc_start: 0.8466 (p0) cc_final: 0.8215 (p0) outliers start: 20 outliers final: 18 residues processed: 81 average time/residue: 0.3141 time to fit residues: 30.2530 Evaluate side-chains 86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130473 restraints weight = 5259.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133795 restraints weight = 3195.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136090 restraints weight = 2196.508| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3394 Z= 0.273 Angle : 0.814 8.306 4615 Z= 0.422 Chirality : 0.052 0.305 490 Planarity : 0.005 0.049 595 Dihedral : 7.751 47.234 516 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.91 % Favored : 85.85 % Rotamer: Outliers : 6.23 % Allowed : 22.95 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.67 (0.39), residues: 417 helix: -4.68 (0.57), residues: 20 sheet: -2.15 (0.40), residues: 167 loop : -2.45 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 353 HIS 0.004 0.002 HIS H 35 PHE 0.022 0.002 PHE F 338 TYR 0.018 0.002 TYR H 104 ARG 0.004 0.001 ARG L 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 1) link_NAG-ASN : angle 3.77323 ( 3) link_BETA1-4 : bond 0.00325 ( 1) link_BETA1-4 : angle 3.64210 ( 3) hydrogen bonds : bond 0.02803 ( 57) hydrogen bonds : angle 7.01630 ( 123) SS BOND : bond 0.00315 ( 3) SS BOND : angle 1.02953 ( 6) covalent geometry : bond 0.00634 ( 3389) covalent geometry : angle 0.80300 ( 4603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3288.15 seconds wall clock time: 61 minutes 16.59 seconds (3676.59 seconds total)