Starting phenix.real_space_refine on Wed Jul 30 04:38:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xxb_33500/07_2025/7xxb_33500_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xxb_33500/07_2025/7xxb_33500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xxb_33500/07_2025/7xxb_33500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xxb_33500/07_2025/7xxb_33500.map" model { file = "/net/cci-nas-00/data/ceres_data/7xxb_33500/07_2025/7xxb_33500_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xxb_33500/07_2025/7xxb_33500_trim.cif" } resolution = 2.93 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 3922 2.51 5 N 940 2.21 5 O 996 1.98 5 H 6138 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12038 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6006 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6006 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.25, per 1000 atoms: 0.52 Number of scatterers: 12038 At special positions: 0 Unit cell: (80.91, 121.83, 69.75, 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 42 16.00 O 996 8.00 N 940 7.00 C 3922 6.00 H 6138 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 961.5 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 79.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 3 through 29 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 35 through 62 removed outlier: 4.943A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.650A pdb=" N ASN A 62 " --> pdb=" O PHE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 68 through 91 Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 126 through 143 Processing helix chain 'A' and resid 143 through 165 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 475 through 492 Processing helix chain 'A' and resid 494 through 513 Processing helix chain 'A' and resid 518 through 530 removed outlier: 4.402A pdb=" N LEU A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 554 through 581 removed outlier: 3.883A pdb=" N GLY A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 584 through 595 Processing helix chain 'A' and resid 599 through 609 removed outlier: 4.035A pdb=" N PHE A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 626 through 640 removed outlier: 3.706A pdb=" N ILE A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 29 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 35 through 62 removed outlier: 4.944A pdb=" N VAL B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.650A pdb=" N ASN B 62 " --> pdb=" O PHE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 92 Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 126 through 143 Processing helix chain 'B' and resid 143 through 165 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 475 through 492 Processing helix chain 'B' and resid 494 through 513 Processing helix chain 'B' and resid 518 through 530 removed outlier: 4.390A pdb=" N LEU B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 547 Processing helix chain 'B' and resid 554 through 581 removed outlier: 3.885A pdb=" N GLY B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) Proline residue: B 570 - end of helix Processing helix chain 'B' and resid 584 through 595 Processing helix chain 'B' and resid 599 through 609 removed outlier: 4.038A pdb=" N PHE B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 626 through 640 removed outlier: 3.690A pdb=" N ILE B 630 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 removed outlier: 7.571A pdb=" N VAL A 204 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE A 175 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL A 206 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 177 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N LYS A 208 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 172 through 177 removed outlier: 7.593A pdb=" N VAL B 204 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE B 175 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL B 206 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL B 177 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LYS B 208 " --> pdb=" O VAL B 177 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1326 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: 4.47 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6132 1.03 - 1.23: 8 1.23 - 1.42: 2460 1.42 - 1.61: 3506 1.61 - 1.81: 78 Bond restraints: 12184 Sorted by residual: bond pdb=" ND2 ASN A 112 " pdb="HD21 ASN A 112 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN B 112 " pdb="HD21 ASN B 112 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN B 112 " pdb="HD22 ASN B 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" ND2 ASN A 112 " pdb="HD22 ASN A 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" N IAC B 701 " pdb=" C IAC B 701 " ideal model delta sigma weight residual 1.363 1.433 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 12179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 22089 5.95 - 11.90: 13 11.90 - 17.85: 0 17.85 - 23.80: 12 23.80 - 29.75: 18 Bond angle restraints: 22132 Sorted by residual: angle pdb=" HZ1 LYS A 158 " pdb=" NZ LYS A 158 " pdb=" HZ3 LYS A 158 " ideal model delta sigma weight residual 109.00 79.25 29.75 3.00e+00 1.11e-01 9.83e+01 angle pdb=" CG LEU A 504 " pdb=" CD2 LEU A 504 " pdb="HD22 LEU A 504 " ideal model delta sigma weight residual 109.00 79.33 29.67 3.00e+00 1.11e-01 9.78e+01 angle pdb=" HZ1 LYS B 158 " pdb=" NZ LYS B 158 " pdb=" HZ3 LYS B 158 " ideal model delta sigma weight residual 109.00 79.33 29.67 3.00e+00 1.11e-01 9.78e+01 angle pdb=" CG LEU B 504 " pdb=" CD2 LEU B 504 " pdb="HD22 LEU B 504 " ideal model delta sigma weight residual 109.00 79.35 29.65 3.00e+00 1.11e-01 9.77e+01 angle pdb=" HZ1 LYS A 158 " pdb=" NZ LYS A 158 " pdb=" HZ2 LYS A 158 " ideal model delta sigma weight residual 109.00 79.39 29.61 3.00e+00 1.11e-01 9.74e+01 ... (remaining 22127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.09: 5011 14.09 - 28.17: 465 28.17 - 42.26: 137 42.26 - 56.35: 73 56.35 - 70.44: 12 Dihedral angle restraints: 5698 sinusoidal: 3054 harmonic: 2644 Sorted by residual: dihedral pdb=" CA LYS A 549 " pdb=" C LYS A 549 " pdb=" N LEU A 550 " pdb=" CA LEU A 550 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LYS B 549 " pdb=" C LYS B 549 " pdb=" N LEU B 550 " pdb=" CA LEU B 550 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA LEU B 625 " pdb=" C LEU B 625 " pdb=" N ILE B 626 " pdb=" CA ILE B 626 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.350: 988 0.350 - 0.700: 0 0.700 - 1.050: 0 1.050 - 1.399: 0 1.399 - 1.749: 2 Chirality restraints: 990 Sorted by residual: chirality pdb=" CG LEU B 550 " pdb=" CB LEU B 550 " pdb=" CD1 LEU B 550 " pdb=" CD2 LEU B 550 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.65e+01 chirality pdb=" CG LEU A 550 " pdb=" CB LEU A 550 " pdb=" CD1 LEU A 550 " pdb=" CD2 LEU A 550 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.28e+01 chirality pdb=" CA ILE A 551 " pdb=" N ILE A 551 " pdb=" C ILE A 551 " pdb=" CB ILE A 551 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 987 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 140 " -0.156 2.00e-02 2.50e+03 1.75e-01 4.60e+02 pdb=" CD GLN A 140 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 140 " 0.150 2.00e-02 2.50e+03 pdb=" NE2 GLN A 140 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 140 " -0.265 2.00e-02 2.50e+03 pdb="HE22 GLN A 140 " 0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 140 " -0.153 2.00e-02 2.50e+03 1.72e-01 4.42e+02 pdb=" CD GLN B 140 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN B 140 " 0.148 2.00e-02 2.50e+03 pdb=" NE2 GLN B 140 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 140 " 0.254 2.00e-02 2.50e+03 pdb="HE22 GLN B 140 " -0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 112 " -0.137 2.00e-02 2.50e+03 1.36e-01 2.78e+02 pdb=" CG ASN A 112 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 112 " 0.131 2.00e-02 2.50e+03 pdb=" ND2 ASN A 112 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 112 " -0.196 2.00e-02 2.50e+03 pdb="HD22 ASN A 112 " 0.191 2.00e-02 2.50e+03 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 714 2.21 - 2.80: 25812 2.80 - 3.40: 35101 3.40 - 4.00: 45022 4.00 - 4.60: 70411 Nonbonded interactions: 177060 Sorted by model distance: nonbonded pdb=" H GLY B 197 " pdb=" O LYS B 201 " model vdw 1.606 2.450 nonbonded pdb=" OE1 GLU A 163 " pdb="HE21 GLN A 164 " model vdw 1.610 2.450 nonbonded pdb=" OE1 GLU B 163 " pdb="HE21 GLN B 164 " model vdw 1.611 2.450 nonbonded pdb=" H GLY A 197 " pdb=" O LYS A 201 " model vdw 1.615 2.450 nonbonded pdb=" O SER A 27 " pdb=" H ILE A 33 " model vdw 1.636 2.450 ... (remaining 177055 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.160 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: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 28.980 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:16.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.004 0.070 6046 Z= 0.175 Angle : 0.677 11.558 8238 Z= 0.343 Chirality : 0.086 1.749 990 Planarity : 0.005 0.053 994 Dihedral : 12.236 70.436 2122 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 0.68 (0.31), residues: 746 helix: 0.91 (0.22), residues: 548 sheet: 0.67 (0.75), residues: 42 loop : -1.01 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 506 HIS 0.004 0.001 HIS A 57 PHE 0.012 0.001 PHE A 603 TYR 0.024 0.002 TYR A 18 ARG 0.008 0.001 ARG B 583 Details of bonding type rmsd hydrogen bonds : bond 0.11605 ( 446) hydrogen bonds : angle 5.83838 ( 1326) covalent geometry : bond 0.00359 ( 6046) covalent geometry : angle 0.67710 ( 8238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 ILE cc_start: 0.8479 (mm) cc_final: 0.8269 (mp) REVERT: A 610 ASN cc_start: 0.8175 (t0) cc_final: 0.7956 (t0) REVERT: B 610 ASN cc_start: 0.8117 (t0) cc_final: 0.7903 (t0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.6139 time to fit residues: 188.2523 Evaluate side-chains 95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138590 restraints weight = 21109.519| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.70 r_work: 0.3538 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6046 Z= 0.158 Angle : 0.594 11.016 8238 Z= 0.306 Chirality : 0.085 1.703 990 Planarity : 0.005 0.039 994 Dihedral : 4.617 33.607 804 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.25 % Allowed : 7.68 % Favored : 91.07 % 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: 0.84 (0.30), residues: 746 helix: 1.02 (0.22), residues: 552 sheet: 0.75 (0.76), residues: 42 loop : -0.98 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 506 HIS 0.003 0.001 HIS A 57 PHE 0.012 0.001 PHE A 45 TYR 0.018 0.001 TYR A 18 ARG 0.005 0.001 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04734 ( 446) hydrogen bonds : angle 5.05913 ( 1326) covalent geometry : bond 0.00352 ( 6046) covalent geometry : angle 0.59431 ( 8238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8209 (ttt180) cc_final: 0.8005 (ttt180) REVERT: A 551 ILE cc_start: 0.8638 (mm) cc_final: 0.8421 (mp) REVERT: A 610 ASN cc_start: 0.8329 (t0) cc_final: 0.8069 (t0) REVERT: B 610 ASN cc_start: 0.8292 (t0) cc_final: 0.8014 (t0) outliers start: 8 outliers final: 2 residues processed: 113 average time/residue: 1.5859 time to fit residues: 193.4714 Evaluate side-chains 99 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain B residue 61 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 0.0040 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.169785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144788 restraints weight = 21309.141| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.72 r_work: 0.3625 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6046 Z= 0.120 Angle : 0.561 10.631 8238 Z= 0.283 Chirality : 0.084 1.695 990 Planarity : 0.005 0.046 994 Dihedral : 4.478 31.011 804 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.10 % Allowed : 8.31 % Favored : 90.60 % 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: 1.05 (0.30), residues: 746 helix: 1.20 (0.22), residues: 550 sheet: 0.95 (0.76), residues: 42 loop : -1.07 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 506 HIS 0.003 0.001 HIS B 57 PHE 0.011 0.001 PHE A 92 TYR 0.018 0.001 TYR B 18 ARG 0.003 0.000 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 446) hydrogen bonds : angle 4.85973 ( 1326) covalent geometry : bond 0.00256 ( 6046) covalent geometry : angle 0.56097 ( 8238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8235 (t0) cc_final: 0.7931 (t0) REVERT: B 44 ARG cc_start: 0.8246 (ttt180) cc_final: 0.7995 (ttt180) REVERT: B 473 MET cc_start: 0.4584 (OUTLIER) cc_final: 0.4230 (ptm) REVERT: B 610 ASN cc_start: 0.8193 (t0) cc_final: 0.7894 (t0) outliers start: 7 outliers final: 1 residues processed: 113 average time/residue: 1.6017 time to fit residues: 195.3773 Evaluate side-chains 101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain B residue 473 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.165541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140400 restraints weight = 21333.923| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.70 r_work: 0.3571 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6046 Z= 0.190 Angle : 0.591 10.512 8238 Z= 0.301 Chirality : 0.086 1.723 990 Planarity : 0.005 0.041 994 Dihedral : 4.556 33.342 804 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.72 % Allowed : 9.40 % Favored : 88.87 % 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: 1.13 (0.30), residues: 746 helix: 1.24 (0.22), residues: 552 sheet: 1.05 (0.77), residues: 42 loop : -1.00 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.004 0.001 HIS A 57 PHE 0.011 0.001 PHE B 45 TYR 0.018 0.002 TYR A 18 ARG 0.007 0.000 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 446) hydrogen bonds : angle 4.80908 ( 1326) covalent geometry : bond 0.00432 ( 6046) covalent geometry : angle 0.59107 ( 8238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8337 (t0) cc_final: 0.8009 (t0) REVERT: B 610 ASN cc_start: 0.8320 (t0) cc_final: 0.7995 (t0) outliers start: 11 outliers final: 2 residues processed: 109 average time/residue: 1.5478 time to fit residues: 182.4266 Evaluate side-chains 100 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 499 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 17 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.166836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141777 restraints weight = 21288.511| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.68 r_work: 0.3586 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6046 Z= 0.144 Angle : 0.568 10.189 8238 Z= 0.286 Chirality : 0.085 1.703 990 Planarity : 0.005 0.041 994 Dihedral : 4.497 33.396 804 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.25 % Allowed : 9.56 % Favored : 89.18 % 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: 1.29 (0.30), residues: 746 helix: 1.34 (0.22), residues: 552 sheet: 1.18 (0.77), residues: 42 loop : -0.89 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.004 0.001 HIS A 57 PHE 0.012 0.001 PHE A 92 TYR 0.010 0.001 TYR B 635 ARG 0.003 0.000 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 446) hydrogen bonds : angle 4.70015 ( 1326) covalent geometry : bond 0.00320 ( 6046) covalent geometry : angle 0.56823 ( 8238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 608 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: A 610 ASN cc_start: 0.8339 (t0) cc_final: 0.7976 (t0) REVERT: B 473 MET cc_start: 0.4679 (OUTLIER) cc_final: 0.4266 (ptm) REVERT: B 608 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6648 (mt-10) REVERT: B 610 ASN cc_start: 0.8311 (t0) cc_final: 0.7959 (t0) outliers start: 8 outliers final: 1 residues processed: 102 average time/residue: 1.5311 time to fit residues: 168.8450 Evaluate side-chains 100 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142698 restraints weight = 21465.396| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.68 r_work: 0.3556 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6046 Z= 0.170 Angle : 0.579 10.220 8238 Z= 0.294 Chirality : 0.085 1.703 990 Planarity : 0.005 0.039 994 Dihedral : 4.531 34.263 804 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.41 % Allowed : 11.13 % Favored : 87.46 % 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: 1.29 (0.30), residues: 746 helix: 1.34 (0.22), residues: 552 sheet: 0.88 (0.78), residues: 44 loop : -0.83 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 506 HIS 0.005 0.001 HIS B 57 PHE 0.014 0.001 PHE B 92 TYR 0.014 0.001 TYR B 635 ARG 0.004 0.000 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 446) hydrogen bonds : angle 4.72231 ( 1326) covalent geometry : bond 0.00385 ( 6046) covalent geometry : angle 0.57898 ( 8238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7123 (t70) cc_final: 0.6650 (t0) REVERT: A 608 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: A 610 ASN cc_start: 0.8402 (t0) cc_final: 0.8014 (t0) REVERT: B 473 MET cc_start: 0.4789 (OUTLIER) cc_final: 0.4412 (ptm) REVERT: B 608 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: B 610 ASN cc_start: 0.8370 (t0) cc_final: 0.7995 (t0) outliers start: 9 outliers final: 2 residues processed: 107 average time/residue: 1.5821 time to fit residues: 182.5706 Evaluate side-chains 105 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.158303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133592 restraints weight = 21668.573| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.61 r_work: 0.3462 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6046 Z= 0.171 Angle : 0.588 10.126 8238 Z= 0.299 Chirality : 0.085 1.706 990 Planarity : 0.005 0.040 994 Dihedral : 4.544 34.890 804 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.63 % Allowed : 12.85 % Favored : 86.52 % 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: 1.28 (0.30), residues: 746 helix: 1.33 (0.21), residues: 552 sheet: 0.94 (0.78), residues: 44 loop : -0.82 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 506 HIS 0.005 0.001 HIS A 57 PHE 0.015 0.001 PHE A 92 TYR 0.015 0.001 TYR B 635 ARG 0.004 0.000 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 446) hydrogen bonds : angle 4.72664 ( 1326) covalent geometry : bond 0.00387 ( 6046) covalent geometry : angle 0.58843 ( 8238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7192 (t70) cc_final: 0.6693 (t0) REVERT: A 608 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: A 610 ASN cc_start: 0.8451 (t0) cc_final: 0.8058 (t0) REVERT: B 473 MET cc_start: 0.4802 (OUTLIER) cc_final: 0.4431 (ptm) REVERT: B 608 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: B 610 ASN cc_start: 0.8445 (t0) cc_final: 0.8059 (t0) outliers start: 4 outliers final: 0 residues processed: 103 average time/residue: 1.5451 time to fit residues: 173.5445 Evaluate side-chains 103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.160501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.136028 restraints weight = 21594.056| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.59 r_work: 0.3483 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6046 Z= 0.120 Angle : 0.560 10.103 8238 Z= 0.280 Chirality : 0.085 1.716 990 Planarity : 0.005 0.040 994 Dihedral : 4.416 33.367 804 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.10 % Allowed : 13.17 % Favored : 85.74 % 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: 1.44 (0.31), residues: 746 helix: 1.46 (0.21), residues: 552 sheet: 1.39 (0.77), residues: 42 loop : -0.93 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 506 HIS 0.003 0.001 HIS A 57 PHE 0.016 0.001 PHE B 92 TYR 0.010 0.001 TYR B 635 ARG 0.001 0.000 ARG B 70 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 446) hydrogen bonds : angle 4.59454 ( 1326) covalent geometry : bond 0.00256 ( 6046) covalent geometry : angle 0.55997 ( 8238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7145 (t70) cc_final: 0.6640 (t0) REVERT: A 608 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: A 610 ASN cc_start: 0.8419 (t0) cc_final: 0.8040 (t0) REVERT: B 65 TYR cc_start: 0.9018 (m-80) cc_final: 0.8803 (m-80) REVERT: B 473 MET cc_start: 0.4687 (OUTLIER) cc_final: 0.4313 (ptm) REVERT: B 608 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: B 610 ASN cc_start: 0.8405 (t0) cc_final: 0.8034 (t0) outliers start: 7 outliers final: 3 residues processed: 111 average time/residue: 1.4176 time to fit residues: 171.0776 Evaluate side-chains 105 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 630 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN B 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.160291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.135643 restraints weight = 21518.579| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.60 r_work: 0.3473 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6046 Z= 0.132 Angle : 0.574 9.872 8238 Z= 0.288 Chirality : 0.085 1.709 990 Planarity : 0.005 0.040 994 Dihedral : 4.363 32.374 804 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.10 % Allowed : 13.01 % Favored : 85.89 % 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: 1.49 (0.31), residues: 746 helix: 1.48 (0.21), residues: 552 sheet: 1.52 (0.78), residues: 42 loop : -0.90 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 506 HIS 0.003 0.001 HIS B 57 PHE 0.012 0.001 PHE A 92 TYR 0.011 0.001 TYR A 635 ARG 0.001 0.000 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 446) hydrogen bonds : angle 4.57188 ( 1326) covalent geometry : bond 0.00290 ( 6046) covalent geometry : angle 0.57364 ( 8238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8115 (ttt180) cc_final: 0.7885 (ttt180) REVERT: A 608 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7059 (mm-30) REVERT: A 610 ASN cc_start: 0.8422 (t0) cc_final: 0.8034 (t0) REVERT: B 473 MET cc_start: 0.4652 (OUTLIER) cc_final: 0.4262 (ptm) REVERT: B 608 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: B 610 ASN cc_start: 0.8404 (t0) cc_final: 0.8027 (t0) outliers start: 7 outliers final: 2 residues processed: 107 average time/residue: 1.5395 time to fit residues: 178.7577 Evaluate side-chains 106 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN B 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135145 restraints weight = 21419.328| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.60 r_work: 0.3458 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6046 Z= 0.140 Angle : 0.578 9.808 8238 Z= 0.290 Chirality : 0.085 1.700 990 Planarity : 0.005 0.040 994 Dihedral : 4.364 32.232 804 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.78 % Allowed : 13.95 % Favored : 85.27 % 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: 1.49 (0.31), residues: 746 helix: 1.49 (0.21), residues: 552 sheet: 1.56 (0.78), residues: 42 loop : -0.92 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 144 HIS 0.003 0.001 HIS A 57 PHE 0.021 0.001 PHE A 92 TYR 0.013 0.001 TYR B 635 ARG 0.002 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 446) hydrogen bonds : angle 4.56708 ( 1326) covalent geometry : bond 0.00309 ( 6046) covalent geometry : angle 0.57766 ( 8238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 608 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: A 610 ASN cc_start: 0.8424 (t0) cc_final: 0.8065 (t0) REVERT: B 473 MET cc_start: 0.4659 (OUTLIER) cc_final: 0.4268 (ptm) REVERT: B 608 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: B 610 ASN cc_start: 0.8420 (t0) cc_final: 0.8041 (t0) outliers start: 5 outliers final: 2 residues processed: 104 average time/residue: 1.9245 time to fit residues: 215.6322 Evaluate side-chains 101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN B 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134821 restraints weight = 21523.593| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.61 r_work: 0.3475 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6046 Z= 0.148 Angle : 0.586 9.762 8238 Z= 0.295 Chirality : 0.085 1.700 990 Planarity : 0.005 0.040 994 Dihedral : 4.367 32.483 804 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.94 % Allowed : 13.79 % Favored : 85.27 % 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: 1.47 (0.31), residues: 746 helix: 1.48 (0.21), residues: 552 sheet: 1.58 (0.78), residues: 42 loop : -0.97 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 144 HIS 0.003 0.001 HIS B 57 PHE 0.010 0.001 PHE B 45 TYR 0.015 0.001 TYR A 635 ARG 0.002 0.000 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 446) hydrogen bonds : angle 4.58110 ( 1326) covalent geometry : bond 0.00329 ( 6046) covalent geometry : angle 0.58601 ( 8238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7981.95 seconds wall clock time: 138 minutes 14.53 seconds (8294.53 seconds total)