Starting phenix.real_space_refine on Thu Jun 5 07:24:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c44_16416/06_2025/8c44_16416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c44_16416/06_2025/8c44_16416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c44_16416/06_2025/8c44_16416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c44_16416/06_2025/8c44_16416.map" model { file = "/net/cci-nas-00/data/ceres_data/8c44_16416/06_2025/8c44_16416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c44_16416/06_2025/8c44_16416.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 3363 2.51 5 N 896 2.21 5 O 952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5239 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3821 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 12, 'TRANS': 445} Chain breaks: 17 Chain: "C" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 158} Chain breaks: 1 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.78, per 1000 atoms: 0.91 Number of scatterers: 5239 At special positions: 0 Unit cell: (64.064, 74.048, 130.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 1 15.00 O 952 8.00 N 896 7.00 C 3363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 553 " distance=2.07 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 710 " distance=2.03 Simple disulfide: pdb=" SG CYS A1027 " - pdb=" SG CYS A1174 " distance=2.04 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 169 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 202 " - " ASN C 47 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 539.1 milliseconds 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1192 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 3 sheets defined 62.1% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 571 through 594 Processing helix chain 'A' and resid 606 through 631 Processing helix chain 'A' and resid 646 through 660 removed outlier: 5.447A pdb=" N PHE A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLN A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 683 Processing helix chain 'A' and resid 694 through 715 removed outlier: 3.572A pdb=" N ASN A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 714 " --> pdb=" O CYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 763 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 869 through 892 Processing helix chain 'A' and resid 904 through 924 Processing helix chain 'A' and resid 931 through 950 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 983 through 990 removed outlier: 3.611A pdb=" N MET A 990 " --> pdb=" O VAL A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.985A pdb=" N HIS A1005 " --> pdb=" O SER A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1012 Processing helix chain 'A' and resid 1013 through 1035 Processing helix chain 'A' and resid 1069 through 1096 removed outlier: 3.743A pdb=" N GLN A1077 " --> pdb=" O THR A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1125 Processing helix chain 'A' and resid 1161 through 1170 Processing helix chain 'C' and resid 58 through 87 Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 141 through 154 removed outlier: 3.502A pdb=" N TYR C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 159 through 167 Processing helix chain 'C' and resid 167 through 176 Processing sheet with id=AA1, first strand: chain 'A' and resid 504 through 506 Processing sheet with id=AA2, first strand: chain 'A' and resid 826 through 828 removed outlier: 3.686A pdb=" N THR A 826 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.647A pdb=" N ALA C 31 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL C 40 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY C 29 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU C 42 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 27 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 25 " --> pdb=" O PRO C 44 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N VAL C 112 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG C 127 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE C 114 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER C 125 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C 116 " --> pdb=" O PHE C 123 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1093 1.32 - 1.46: 1702 1.46 - 1.59: 2499 1.59 - 1.72: 24 1.72 - 1.85: 34 Bond restraints: 5352 Sorted by residual: bond pdb=" C THR A1154 " pdb=" N PRO A1155 " ideal model delta sigma weight residual 1.331 1.396 -0.065 1.31e-02 5.83e+03 2.50e+01 bond pdb=" N VAL C 124 " pdb=" CA VAL C 124 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.07e-02 8.73e+03 2.17e+01 bond pdb=" C ILE A 639 " pdb=" N PRO A 640 " ideal model delta sigma weight residual 1.330 1.386 -0.056 1.22e-02 6.72e+03 2.13e+01 bond pdb=" N PRO A 640 " pdb=" CD PRO A 640 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" CB ILE A1012 " pdb=" CG1 ILE A1012 " ideal model delta sigma weight residual 1.530 1.451 0.079 2.00e-02 2.50e+03 1.54e+01 ... (remaining 5347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 6977 3.97 - 7.94: 201 7.94 - 11.91: 9 11.91 - 15.88: 0 15.88 - 19.85: 2 Bond angle restraints: 7189 Sorted by residual: angle pdb=" N PRO C 22 " pdb=" CA PRO C 22 " pdb=" C PRO C 22 " ideal model delta sigma weight residual 113.53 102.47 11.06 1.39e+00 5.18e-01 6.33e+01 angle pdb=" C THR A1006 " pdb=" N PRO A1007 " pdb=" CA PRO A1007 " ideal model delta sigma weight residual 120.21 127.27 -7.06 9.60e-01 1.09e+00 5.41e+01 angle pdb=" C ARG C 127 " pdb=" N PRO C 128 " pdb=" CA PRO C 128 " ideal model delta sigma weight residual 119.84 128.85 -9.01 1.25e+00 6.40e-01 5.20e+01 angle pdb=" C GLY C 43 " pdb=" N PRO C 44 " pdb=" CA PRO C 44 " ideal model delta sigma weight residual 120.21 126.84 -6.63 9.60e-01 1.09e+00 4.77e+01 angle pdb=" C THR A 823 " pdb=" N PRO A 824 " pdb=" CA PRO A 824 " ideal model delta sigma weight residual 119.78 126.72 -6.94 1.03e+00 9.43e-01 4.54e+01 ... (remaining 7184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.24: 3152 32.24 - 64.48: 62 64.48 - 96.71: 7 96.71 - 128.95: 0 128.95 - 161.19: 1 Dihedral angle restraints: 3222 sinusoidal: 1394 harmonic: 1828 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 710 " pdb=" CB CYS A 710 " ideal model delta sinusoidal sigma weight residual -86.00 -174.59 88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" C3 PTY C 201 " pdb=" O11 PTY C 201 " pdb=" P1 PTY C 201 " pdb=" O12 PTY C 201 " ideal model delta sinusoidal sigma weight residual 300.23 139.04 161.19 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CD ARG C 20 " pdb=" NE ARG C 20 " pdb=" CZ ARG C 20 " pdb=" NH1 ARG C 20 " ideal model delta sinusoidal sigma weight residual 0.00 -36.88 36.88 1 1.00e+01 1.00e-02 1.92e+01 ... (remaining 3219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 519 0.095 - 0.191: 202 0.191 - 0.286: 32 0.286 - 0.381: 1 0.381 - 0.477: 3 Chirality restraints: 757 Sorted by residual: chirality pdb=" CB ILE A 639 " pdb=" CA ILE A 639 " pdb=" CG1 ILE A 639 " pdb=" CG2 ILE A 639 " both_signs ideal model delta sigma weight residual False 2.64 3.12 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C2 NAG C 202 " pdb=" C1 NAG C 202 " pdb=" C3 NAG C 202 " pdb=" N2 NAG C 202 " both_signs ideal model delta sigma weight residual False -2.49 -2.91 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C1 NAG C 202 " pdb=" ND2 ASN C 47 " pdb=" C2 NAG C 202 " pdb=" O5 NAG C 202 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-01 2.50e+01 4.10e+00 ... (remaining 754 not shown) Planarity restraints: 895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 20 " 0.647 9.50e-02 1.11e+02 2.90e-01 5.13e+01 pdb=" NE ARG C 20 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG C 20 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 20 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 20 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1017 " -0.556 9.50e-02 1.11e+02 2.49e-01 3.79e+01 pdb=" NE ARG A1017 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A1017 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A1017 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1017 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 176 " 0.026 2.00e-02 2.50e+03 5.22e-02 2.72e+01 pdb=" C HIS C 176 " -0.090 2.00e-02 2.50e+03 pdb=" O HIS C 176 " 0.032 2.00e-02 2.50e+03 pdb=" OXT HIS C 176 " 0.032 2.00e-02 2.50e+03 ... (remaining 892 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1746 2.85 - 3.36: 5164 3.36 - 3.87: 9284 3.87 - 4.39: 10847 4.39 - 4.90: 17208 Nonbonded interactions: 44249 Sorted by model distance: nonbonded pdb=" NZ LYS A1015 " pdb=" OD1 ASP A1112 " model vdw 2.336 3.120 nonbonded pdb=" NZ LYS A 745 " pdb=" OD1 ASP A1009 " model vdw 2.388 3.120 nonbonded pdb=" N ASP A 984 " pdb=" OD1 ASP A 984 " model vdw 2.407 3.120 nonbonded pdb=" NZ LYS A 827 " pdb=" OE2 GLU A 838 " model vdw 2.421 3.120 nonbonded pdb=" OD2 ASP A 572 " pdb=" NZ LYS A 642 " model vdw 2.444 3.120 ... (remaining 44244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.440 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 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 : 0.020 0.123 5358 Z= 1.057 Angle : 1.661 19.848 7202 Z= 1.122 Chirality : 0.098 0.477 757 Planarity : 0.015 0.290 894 Dihedral : 12.787 161.189 2015 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.54 % Allowed : 2.86 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.28 (0.34), residues: 584 helix: 1.44 (0.26), residues: 331 sheet: 0.62 (0.66), residues: 57 loop : 0.03 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.008 TRP C 133 HIS 0.007 0.002 HIS A1167 PHE 0.025 0.005 PHE A 615 TYR 0.047 0.007 TYR C 154 ARG 0.007 0.001 ARG A 975 Details of bonding type rmsd link_NAG-ASN : bond 0.08466 ( 1) link_NAG-ASN : angle 2.47573 ( 3) hydrogen bonds : bond 0.17074 ( 331) hydrogen bonds : angle 7.09321 ( 948) SS BOND : bond 0.02808 ( 5) SS BOND : angle 2.95485 ( 10) covalent geometry : bond 0.01983 ( 5352) covalent geometry : angle 1.65854 ( 7189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 182 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7285 (mttt) cc_final: 0.6984 (mmtm) REVERT: A 1172 MET cc_start: 0.7568 (mmp) cc_final: 0.6645 (mmt) REVERT: C 75 GLN cc_start: 0.7771 (mt0) cc_final: 0.7216 (tt0) REVERT: C 160 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6412 (mt-10) outliers start: 3 outliers final: 1 residues processed: 185 average time/residue: 0.2514 time to fit residues: 55.4639 Evaluate side-chains 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1174 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN A 611 ASN A 621 GLN A 716 ASN A 746 GLN A 749 GLN C 85 GLN C 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.216194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.180323 restraints weight = 5872.010| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.90 r_work: 0.4079 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5358 Z= 0.179 Angle : 0.631 6.448 7202 Z= 0.350 Chirality : 0.043 0.189 757 Planarity : 0.005 0.043 894 Dihedral : 9.284 150.525 728 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.14 % Allowed : 8.93 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.15 (0.34), residues: 584 helix: 2.37 (0.26), residues: 348 sheet: -0.05 (0.54), residues: 72 loop : 0.11 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 669 HIS 0.011 0.002 HIS C 84 PHE 0.018 0.002 PHE A 651 TYR 0.024 0.002 TYR A1120 ARG 0.007 0.001 ARG C 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 1) link_NAG-ASN : angle 1.49894 ( 3) hydrogen bonds : bond 0.05165 ( 331) hydrogen bonds : angle 4.92726 ( 948) SS BOND : bond 0.01168 ( 5) SS BOND : angle 1.83374 ( 10) covalent geometry : bond 0.00404 ( 5352) covalent geometry : angle 0.62731 ( 7189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6729 (mttt) cc_final: 0.5813 (mmtm) REVERT: A 761 GLU cc_start: 0.6997 (tt0) cc_final: 0.6620 (mt-10) REVERT: A 840 PHE cc_start: 0.7898 (m-80) cc_final: 0.7427 (m-80) REVERT: A 882 LYS cc_start: 0.6618 (tttt) cc_final: 0.6270 (tptm) REVERT: A 883 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7678 (mt-10) REVERT: A 1090 LYS cc_start: 0.6972 (tppt) cc_final: 0.5837 (pttp) REVERT: A 1172 MET cc_start: 0.7597 (mmp) cc_final: 0.6761 (mmp) REVERT: C 42 GLU cc_start: 0.7708 (tt0) cc_final: 0.7323 (tt0) outliers start: 12 outliers final: 7 residues processed: 132 average time/residue: 0.2751 time to fit residues: 44.2123 Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 714 ASN C 52 GLN ** C 85 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 = 0.4540 r_free = 0.4540 target = 0.206135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.171998 restraints weight = 5966.856| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.80 r_work: 0.4044 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5358 Z= 0.152 Angle : 0.569 9.088 7202 Z= 0.310 Chirality : 0.040 0.152 757 Planarity : 0.004 0.036 894 Dihedral : 7.985 118.976 728 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.50 % Allowed : 13.04 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.10 (0.34), residues: 584 helix: 2.39 (0.26), residues: 353 sheet: -0.57 (0.54), residues: 73 loop : 0.15 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 978 HIS 0.005 0.001 HIS C 84 PHE 0.013 0.002 PHE A 651 TYR 0.014 0.002 TYR C 27 ARG 0.006 0.000 ARG C 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 1) link_NAG-ASN : angle 1.88264 ( 3) hydrogen bonds : bond 0.04372 ( 331) hydrogen bonds : angle 4.56691 ( 948) SS BOND : bond 0.00323 ( 5) SS BOND : angle 1.32783 ( 10) covalent geometry : bond 0.00342 ( 5352) covalent geometry : angle 0.56603 ( 7189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6804 (mttt) cc_final: 0.6073 (mmtm) REVERT: A 761 GLU cc_start: 0.7142 (tt0) cc_final: 0.6850 (mt-10) REVERT: A 840 PHE cc_start: 0.7938 (m-80) cc_final: 0.7540 (m-80) REVERT: A 882 LYS cc_start: 0.6653 (tttt) cc_final: 0.6303 (tptm) REVERT: A 915 TYR cc_start: 0.8424 (t80) cc_final: 0.7694 (t80) REVERT: A 1090 LYS cc_start: 0.6637 (tppt) cc_final: 0.5683 (pttp) REVERT: C 150 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7304 (mt0) outliers start: 14 outliers final: 9 residues processed: 111 average time/residue: 0.1975 time to fit residues: 27.7087 Evaluate side-chains 84 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 756 HIS ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.208576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.172166 restraints weight = 6081.755| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.97 r_work: 0.4008 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5358 Z= 0.199 Angle : 0.612 11.176 7202 Z= 0.328 Chirality : 0.042 0.178 757 Planarity : 0.004 0.033 894 Dihedral : 7.796 103.262 728 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.50 % Allowed : 13.57 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.68 (0.34), residues: 584 helix: 2.11 (0.26), residues: 353 sheet: -0.83 (0.54), residues: 73 loop : -0.11 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 669 HIS 0.004 0.001 HIS A 756 PHE 0.020 0.002 PHE A 655 TYR 0.020 0.002 TYR A 595 ARG 0.004 0.001 ARG C 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00008 ( 1) link_NAG-ASN : angle 2.03309 ( 3) hydrogen bonds : bond 0.04502 ( 331) hydrogen bonds : angle 4.67845 ( 948) SS BOND : bond 0.00346 ( 5) SS BOND : angle 1.74833 ( 10) covalent geometry : bond 0.00466 ( 5352) covalent geometry : angle 0.60766 ( 7189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6862 (mttt) cc_final: 0.6072 (mmtm) REVERT: A 761 GLU cc_start: 0.7118 (tt0) cc_final: 0.6772 (mt-10) REVERT: A 840 PHE cc_start: 0.7996 (m-80) cc_final: 0.7632 (m-80) REVERT: A 882 LYS cc_start: 0.6846 (tttt) cc_final: 0.6330 (tptm) REVERT: A 1090 LYS cc_start: 0.6579 (tppt) cc_final: 0.5613 (pttt) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.2515 time to fit residues: 35.0712 Evaluate side-chains 94 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.206857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.170680 restraints weight = 5994.991| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 2.91 r_work: 0.3973 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5358 Z= 0.216 Angle : 0.636 9.261 7202 Z= 0.339 Chirality : 0.042 0.165 757 Planarity : 0.004 0.034 894 Dihedral : 7.639 88.344 728 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.32 % Allowed : 16.43 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.29 (0.34), residues: 584 helix: 1.81 (0.26), residues: 352 sheet: -1.09 (0.56), residues: 73 loop : -0.20 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 669 HIS 0.003 0.001 HIS A1167 PHE 0.018 0.002 PHE A 655 TYR 0.021 0.002 TYR A 595 ARG 0.003 0.001 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 1) link_NAG-ASN : angle 2.09096 ( 3) hydrogen bonds : bond 0.04553 ( 331) hydrogen bonds : angle 4.69399 ( 948) SS BOND : bond 0.00470 ( 5) SS BOND : angle 1.73754 ( 10) covalent geometry : bond 0.00506 ( 5352) covalent geometry : angle 0.63170 ( 7189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6648 (mttt) cc_final: 0.5938 (mmtm) REVERT: A 761 GLU cc_start: 0.7085 (tt0) cc_final: 0.6772 (mt-10) REVERT: A 840 PHE cc_start: 0.8026 (m-80) cc_final: 0.7760 (m-80) REVERT: A 882 LYS cc_start: 0.6811 (tttt) cc_final: 0.6322 (tptm) REVERT: A 1090 LYS cc_start: 0.6542 (tppt) cc_final: 0.5554 (pttt) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 0.1881 time to fit residues: 23.5244 Evaluate side-chains 89 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.0470 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.210184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.173948 restraints weight = 6018.478| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.93 r_work: 0.4025 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5358 Z= 0.151 Angle : 0.562 8.169 7202 Z= 0.305 Chirality : 0.040 0.165 757 Planarity : 0.004 0.038 894 Dihedral : 7.194 73.213 728 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.04 % Allowed : 15.00 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.60 (0.35), residues: 584 helix: 2.03 (0.27), residues: 354 sheet: -1.21 (0.56), residues: 73 loop : 0.07 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 669 HIS 0.003 0.001 HIS A1167 PHE 0.024 0.002 PHE C 123 TYR 0.019 0.002 TYR A 595 ARG 0.004 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00009 ( 1) link_NAG-ASN : angle 1.81556 ( 3) hydrogen bonds : bond 0.04077 ( 331) hydrogen bonds : angle 4.48611 ( 948) SS BOND : bond 0.00340 ( 5) SS BOND : angle 1.16914 ( 10) covalent geometry : bond 0.00345 ( 5352) covalent geometry : angle 0.55969 ( 7189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6629 (mttt) cc_final: 0.5891 (mmtm) REVERT: A 664 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7377 (mm-30) REVERT: A 840 PHE cc_start: 0.7975 (m-80) cc_final: 0.7654 (m-80) REVERT: A 882 LYS cc_start: 0.6821 (tttt) cc_final: 0.6170 (tppt) REVERT: A 915 TYR cc_start: 0.8482 (t80) cc_final: 0.7689 (t80) REVERT: A 1090 LYS cc_start: 0.6594 (tppt) cc_final: 0.5566 (pttt) REVERT: C 175 LYS cc_start: 0.8663 (mttp) cc_final: 0.8368 (mttp) outliers start: 17 outliers final: 12 residues processed: 103 average time/residue: 0.1895 time to fit residues: 25.0347 Evaluate side-chains 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 43 optimal weight: 0.0870 chunk 33 optimal weight: 0.4980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.203133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.169325 restraints weight = 5951.893| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.77 r_work: 0.4023 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5358 Z= 0.141 Angle : 0.543 7.666 7202 Z= 0.295 Chirality : 0.040 0.169 757 Planarity : 0.004 0.060 894 Dihedral : 6.914 60.735 728 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 17.14 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.61 (0.35), residues: 584 helix: 2.11 (0.27), residues: 354 sheet: -1.23 (0.57), residues: 74 loop : -0.06 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 669 HIS 0.003 0.001 HIS A1167 PHE 0.030 0.002 PHE A 655 TYR 0.017 0.002 TYR A 595 ARG 0.003 0.000 ARG C 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00008 ( 1) link_NAG-ASN : angle 1.71242 ( 3) hydrogen bonds : bond 0.03892 ( 331) hydrogen bonds : angle 4.33847 ( 948) SS BOND : bond 0.00343 ( 5) SS BOND : angle 1.30700 ( 10) covalent geometry : bond 0.00318 ( 5352) covalent geometry : angle 0.53984 ( 7189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6681 (mttt) cc_final: 0.6374 (mttm) REVERT: A 840 PHE cc_start: 0.7937 (m-80) cc_final: 0.7638 (m-80) REVERT: A 882 LYS cc_start: 0.6782 (tttt) cc_final: 0.6210 (tppt) REVERT: A 891 LYS cc_start: 0.7507 (mttt) cc_final: 0.7295 (mmtt) REVERT: A 915 TYR cc_start: 0.8445 (t80) cc_final: 0.7685 (t80) REVERT: A 1090 LYS cc_start: 0.6561 (tppt) cc_final: 0.5609 (pttt) outliers start: 11 outliers final: 9 residues processed: 96 average time/residue: 0.1841 time to fit residues: 22.7346 Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 0.0870 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 985 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.206690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.173245 restraints weight = 5927.339| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 2.74 r_work: 0.4069 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5358 Z= 0.116 Angle : 0.517 7.268 7202 Z= 0.280 Chirality : 0.039 0.163 757 Planarity : 0.004 0.058 894 Dihedral : 6.568 50.956 728 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 17.86 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.93 (0.36), residues: 584 helix: 2.39 (0.27), residues: 353 sheet: -1.24 (0.56), residues: 74 loop : 0.07 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 979 HIS 0.003 0.001 HIS A1167 PHE 0.029 0.002 PHE A 655 TYR 0.016 0.001 TYR A 595 ARG 0.004 0.000 ARG C 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 1.45509 ( 3) hydrogen bonds : bond 0.03554 ( 331) hydrogen bonds : angle 4.17064 ( 948) SS BOND : bond 0.00306 ( 5) SS BOND : angle 1.01323 ( 10) covalent geometry : bond 0.00256 ( 5352) covalent geometry : angle 0.51486 ( 7189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6645 (mttt) cc_final: 0.6316 (mttm) REVERT: A 840 PHE cc_start: 0.7907 (m-80) cc_final: 0.7590 (m-80) REVERT: A 882 LYS cc_start: 0.6842 (tttt) cc_final: 0.6326 (tppt) REVERT: A 915 TYR cc_start: 0.8485 (t80) cc_final: 0.7739 (t80) REVERT: A 1090 LYS cc_start: 0.6554 (tppt) cc_final: 0.5631 (pttt) REVERT: A 1172 MET cc_start: 0.6918 (mmt) cc_final: 0.6608 (mmt) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.1753 time to fit residues: 21.1068 Evaluate side-chains 85 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.0470 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.202033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.168630 restraints weight = 5939.079| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.71 r_work: 0.4020 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5358 Z= 0.157 Angle : 0.560 7.418 7202 Z= 0.303 Chirality : 0.040 0.177 757 Planarity : 0.004 0.053 894 Dihedral : 6.778 52.134 728 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.14 % Allowed : 18.04 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.72 (0.35), residues: 584 helix: 2.22 (0.27), residues: 354 sheet: -0.89 (0.58), residues: 69 loop : -0.31 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 978 HIS 0.003 0.001 HIS A1167 PHE 0.027 0.002 PHE A 655 TYR 0.017 0.002 TYR A1120 ARG 0.004 0.000 ARG C 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 1.63414 ( 3) hydrogen bonds : bond 0.03919 ( 331) hydrogen bonds : angle 4.36673 ( 948) SS BOND : bond 0.00338 ( 5) SS BOND : angle 1.15268 ( 10) covalent geometry : bond 0.00363 ( 5352) covalent geometry : angle 0.55800 ( 7189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6710 (mttt) cc_final: 0.6389 (mttm) REVERT: A 840 PHE cc_start: 0.8018 (m-80) cc_final: 0.7728 (m-80) REVERT: A 882 LYS cc_start: 0.6859 (tttt) cc_final: 0.6277 (tppt) REVERT: A 1090 LYS cc_start: 0.6519 (tppt) cc_final: 0.5588 (pttt) REVERT: A 1172 MET cc_start: 0.7018 (mmt) cc_final: 0.6475 (mmt) REVERT: C 175 LYS cc_start: 0.8789 (mttp) cc_final: 0.8533 (mtmp) outliers start: 12 outliers final: 11 residues processed: 95 average time/residue: 0.1874 time to fit residues: 22.9109 Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.0030 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.203671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.170068 restraints weight = 5968.624| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.74 r_work: 0.4036 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5358 Z= 0.140 Angle : 0.543 7.262 7202 Z= 0.296 Chirality : 0.039 0.170 757 Planarity : 0.004 0.053 894 Dihedral : 6.678 51.668 728 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.14 % Allowed : 17.86 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.69 (0.36), residues: 584 helix: 2.27 (0.27), residues: 354 sheet: -1.32 (0.56), residues: 74 loop : -0.24 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 978 HIS 0.003 0.001 HIS A1167 PHE 0.028 0.002 PHE A 655 TYR 0.016 0.002 TYR A 595 ARG 0.003 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00026 ( 1) link_NAG-ASN : angle 1.59607 ( 3) hydrogen bonds : bond 0.03779 ( 331) hydrogen bonds : angle 4.29313 ( 948) SS BOND : bond 0.00301 ( 5) SS BOND : angle 1.51044 ( 10) covalent geometry : bond 0.00318 ( 5352) covalent geometry : angle 0.53943 ( 7189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6708 (mttt) cc_final: 0.6399 (mttm) REVERT: A 840 PHE cc_start: 0.8012 (m-80) cc_final: 0.7697 (m-80) REVERT: A 882 LYS cc_start: 0.6838 (tttt) cc_final: 0.6335 (tppt) REVERT: A 1090 LYS cc_start: 0.6508 (tppt) cc_final: 0.5554 (pttt) REVERT: A 1172 MET cc_start: 0.6952 (mmt) cc_final: 0.6543 (mmt) REVERT: C 175 LYS cc_start: 0.8805 (mttp) cc_final: 0.8588 (mtmp) outliers start: 12 outliers final: 11 residues processed: 90 average time/residue: 0.1716 time to fit residues: 20.5583 Evaluate side-chains 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.200877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.166884 restraints weight = 6031.506| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.75 r_work: 0.3997 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5358 Z= 0.178 Angle : 0.598 7.586 7202 Z= 0.324 Chirality : 0.041 0.181 757 Planarity : 0.004 0.051 894 Dihedral : 6.892 52.402 728 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.32 % Allowed : 17.86 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.48 (0.35), residues: 584 helix: 2.09 (0.27), residues: 354 sheet: -1.08 (0.59), residues: 69 loop : -0.51 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 978 HIS 0.003 0.001 HIS A1167 PHE 0.026 0.002 PHE A 655 TYR 0.017 0.002 TYR A1120 ARG 0.004 0.001 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00003 ( 1) link_NAG-ASN : angle 1.75470 ( 3) hydrogen bonds : bond 0.04104 ( 331) hydrogen bonds : angle 4.41716 ( 948) SS BOND : bond 0.00437 ( 5) SS BOND : angle 1.64703 ( 10) covalent geometry : bond 0.00415 ( 5352) covalent geometry : angle 0.59396 ( 7189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3529.15 seconds wall clock time: 62 minutes 39.48 seconds (3759.48 seconds total)