Starting phenix.real_space_refine on Fri Mar 15 15:08:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxb_33500/03_2024/7xxb_33500_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxb_33500/03_2024/7xxb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxb_33500/03_2024/7xxb_33500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxb_33500/03_2024/7xxb_33500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxb_33500/03_2024/7xxb_33500_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxb_33500/03_2024/7xxb_33500_trim_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.68, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 10.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 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... running ksdssp... Secondary structure from input PDB file: 34 helices and 2 sheets defined 72.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 36 through 61 removed outlier: 4.943A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 69 through 90 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 144 through 164 Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 476 through 493 removed outlier: 4.049A pdb=" N ARG A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 Processing helix chain 'A' and resid 519 through 529 removed outlier: 4.402A pdb=" N LEU A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 546 Processing helix chain 'A' and resid 555 through 580 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 585 through 594 Processing helix chain 'A' and resid 601 through 609 Processing helix chain 'A' and resid 613 through 639 removed outlier: 4.645A pdb=" N LEU A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'B' and resid 4 through 29 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 36 through 61 removed outlier: 4.944A pdb=" N VAL B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 69 through 91 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 116 through 124 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 144 through 164 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 476 through 493 removed outlier: 4.052A pdb=" N ARG B 493 " --> pdb=" O ARG B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 512 Processing helix chain 'B' and resid 519 through 529 removed outlier: 4.390A pdb=" N LEU B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 546 Processing helix chain 'B' and resid 555 through 580 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 585 through 594 Processing helix chain 'B' and resid 601 through 609 Processing helix chain 'B' and resid 613 through 639 removed outlier: 4.656A pdb=" N LEU B 628 " --> pdb=" O MET B 624 " (cutoff:3.500A) Proline residue: B 629 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 175 through 177 removed outlier: 9.075A pdb=" N LYS A 176 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A 204 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 175 through 177 removed outlier: 9.057A pdb=" N LYS B 176 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL B 204 " --> pdb=" O LYS B 176 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1173 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: 4.76 Time building geometry restraints manager: 10.46 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: 79.25 - 91.10: 22 91.10 - 102.94: 41 102.94 - 114.79: 15570 114.79 - 126.64: 6377 126.64 - 138.49: 122 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: 735 2.21 - 2.80: 25854 2.80 - 3.40: 35142 3.40 - 4.00: 45106 4.00 - 4.60: 70496 Nonbonded interactions: 177333 Sorted by model distance: nonbonded pdb=" H GLY B 197 " pdb=" O LYS B 201 " model vdw 1.606 1.850 nonbonded pdb=" OE1 GLU A 163 " pdb="HE21 GLN A 164 " model vdw 1.610 1.850 nonbonded pdb=" OE1 GLU B 163 " pdb="HE21 GLN B 164 " model vdw 1.611 1.850 nonbonded pdb=" H GLY A 197 " pdb=" O LYS A 201 " model vdw 1.615 1.850 nonbonded pdb=" O SER A 27 " pdb=" H ILE A 33 " model vdw 1.636 1.850 ... (remaining 177328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 3.620 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 42.290 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.800 ------------------------------------------------------------------------------- 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= 0.232 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.899 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: 1.5176 time to fit residues: 176.9429 Evaluate side-chains 95 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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: 0.5980 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.0705 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= 0.186 Angle : 0.555 11.037 8238 Z= 0.274 Chirality : 0.084 1.699 990 Planarity : 0.004 0.037 994 Dihedral : 4.430 27.163 804 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.10 % Allowed : 6.90 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.31), residues: 746 helix: 1.06 (0.22), residues: 544 sheet: 0.93 (0.76), residues: 42 loop : -1.17 (0.48), residues: 160 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 0.015 0.001 TYR A 18 ARG 0.004 0.001 ARG A 583 *********************** 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 105 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8162 (t0) cc_final: 0.7959 (t0) REVERT: B 610 ASN cc_start: 0.8130 (t0) cc_final: 0.7907 (t0) outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 1.4380 time to fit residues: 160.9829 Evaluate side-chains 99 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 499 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0928 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= 0.221 Angle : 0.555 10.846 8238 Z= 0.276 Chirality : 0.085 1.706 990 Planarity : 0.004 0.037 994 Dihedral : 4.345 25.560 804 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.72 % Allowed : 7.84 % Favored : 90.44 % 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: 1.00 (0.31), residues: 746 helix: 1.17 (0.22), residues: 546 sheet: 1.22 (0.78), residues: 42 loop : -1.09 (0.49), residues: 158 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 0.011 0.001 TYR A 18 ARG 0.004 0.000 ARG A 565 *********************** 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 109 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8190 (t0) cc_final: 0.7937 (t0) REVERT: B 610 ASN cc_start: 0.8198 (t0) cc_final: 0.7948 (t0) outliers start: 11 outliers final: 4 residues processed: 106 average time/residue: 1.4965 time to fit residues: 171.6037 Evaluate side-chains 100 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 499 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6046 Z= 0.233 Angle : 0.560 10.384 8238 Z= 0.278 Chirality : 0.084 1.693 990 Planarity : 0.004 0.038 994 Dihedral : 4.353 27.167 804 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.04 % Allowed : 9.25 % Favored : 88.71 % 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: 1.03 (0.31), residues: 746 helix: 1.19 (0.22), residues: 546 sheet: 1.31 (0.78), residues: 42 loop : -1.15 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 506 HIS 0.004 0.001 HIS A 57 PHE 0.012 0.001 PHE B 45 TYR 0.012 0.001 TYR B 635 ARG 0.004 0.000 ARG A 565 *********************** 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 111 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 608 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: A 610 ASN cc_start: 0.8254 (t0) cc_final: 0.7998 (t0) REVERT: B 608 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6416 (mt-10) REVERT: B 610 ASN cc_start: 0.8263 (t0) cc_final: 0.7991 (t0) outliers start: 13 outliers final: 4 residues processed: 105 average time/residue: 1.5435 time to fit residues: 174.7627 Evaluate side-chains 101 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1252 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= 0.203 Angle : 0.549 10.338 8238 Z= 0.271 Chirality : 0.084 1.699 990 Planarity : 0.004 0.039 994 Dihedral : 4.291 27.194 804 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.41 % Allowed : 10.34 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.31), residues: 746 helix: 1.32 (0.22), residues: 546 sheet: 1.43 (0.78), residues: 42 loop : -1.03 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.004 0.001 HIS B 57 PHE 0.013 0.001 PHE A 92 TYR 0.012 0.001 TYR B 635 ARG 0.003 0.000 ARG A 44 *********************** 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 106 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8242 (t0) cc_final: 0.7966 (t0) REVERT: B 608 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6388 (mt-10) REVERT: B 610 ASN cc_start: 0.8274 (t0) cc_final: 0.7980 (t0) outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 1.4734 time to fit residues: 161.0362 Evaluate side-chains 98 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 499 SER 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 24 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6046 Z= 0.203 Angle : 0.543 10.242 8238 Z= 0.269 Chirality : 0.084 1.702 990 Planarity : 0.004 0.039 994 Dihedral : 4.261 27.106 804 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.88 % Allowed : 10.50 % Favored : 87.62 % 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: 1.34 (0.31), residues: 746 helix: 1.39 (0.22), residues: 548 sheet: 1.54 (0.78), residues: 42 loop : -0.98 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 506 HIS 0.004 0.001 HIS B 57 PHE 0.012 0.001 PHE A 45 TYR 0.013 0.001 TYR B 635 ARG 0.003 0.000 ARG A 565 *********************** 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 109 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8264 (t0) cc_final: 0.7942 (t0) REVERT: B 608 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6377 (mt-10) REVERT: B 610 ASN cc_start: 0.8302 (t0) cc_final: 0.8000 (t0) outliers start: 12 outliers final: 5 residues processed: 104 average time/residue: 1.4130 time to fit residues: 159.5030 Evaluate side-chains 100 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 575 VAL 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 69 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1503 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= 0.213 Angle : 0.553 10.178 8238 Z= 0.276 Chirality : 0.084 1.699 990 Planarity : 0.004 0.039 994 Dihedral : 4.277 27.159 804 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.25 % Allowed : 11.60 % Favored : 87.15 % 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: 1.36 (0.31), residues: 746 helix: 1.40 (0.22), residues: 548 sheet: 1.59 (0.77), residues: 42 loop : -0.98 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 506 HIS 0.004 0.001 HIS B 57 PHE 0.015 0.001 PHE B 92 TYR 0.012 0.001 TYR B 635 ARG 0.003 0.000 ARG A 565 *********************** 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 106 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8312 (t0) cc_final: 0.7990 (t0) REVERT: B 473 MET cc_start: 0.4406 (OUTLIER) cc_final: 0.3903 (ptm) REVERT: B 608 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6402 (mt-10) REVERT: B 610 ASN cc_start: 0.8299 (t0) cc_final: 0.7955 (t0) REVERT: B 635 TYR cc_start: 0.7261 (t80) cc_final: 0.6756 (t80) outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 1.4597 time to fit residues: 159.8739 Evaluate side-chains 103 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 61 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.0570 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.0040 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6046 Z= 0.155 Angle : 0.530 10.040 8238 Z= 0.260 Chirality : 0.084 1.704 990 Planarity : 0.004 0.040 994 Dihedral : 4.141 25.723 804 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.25 % Allowed : 11.29 % 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: 1.62 (0.31), residues: 746 helix: 1.57 (0.22), residues: 548 sheet: 1.76 (0.79), residues: 42 loop : -0.79 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 506 HIS 0.002 0.000 HIS A 57 PHE 0.017 0.001 PHE A 92 TYR 0.018 0.001 TYR A 635 ARG 0.001 0.000 ARG A 44 *********************** 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 109 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8259 (t0) cc_final: 0.7966 (t0) REVERT: A 635 TYR cc_start: 0.6426 (t80) cc_final: 0.6196 (t80) REVERT: B 473 MET cc_start: 0.4447 (OUTLIER) cc_final: 0.3955 (ptm) REVERT: B 608 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: B 610 ASN cc_start: 0.8268 (t0) cc_final: 0.7947 (t0) REVERT: B 635 TYR cc_start: 0.7274 (t80) cc_final: 0.6769 (t80) outliers start: 8 outliers final: 2 residues processed: 105 average time/residue: 1.5045 time to fit residues: 170.8310 Evaluate side-chains 102 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 608 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1710 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= 0.246 Angle : 0.561 9.880 8238 Z= 0.282 Chirality : 0.084 1.692 990 Planarity : 0.004 0.039 994 Dihedral : 4.239 26.435 804 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.94 % Allowed : 12.07 % Favored : 86.99 % 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: 1.40 (0.31), residues: 746 helix: 1.43 (0.22), residues: 548 sheet: 1.81 (0.79), residues: 42 loop : -1.03 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 506 HIS 0.004 0.001 HIS B 57 PHE 0.018 0.001 PHE B 92 TYR 0.013 0.001 TYR B 635 ARG 0.003 0.000 ARG A 565 *********************** 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 106 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8330 (t0) cc_final: 0.8006 (t0) REVERT: B 473 MET cc_start: 0.4532 (OUTLIER) cc_final: 0.4074 (ptm) REVERT: B 608 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: B 610 ASN cc_start: 0.8315 (t0) cc_final: 0.7953 (t0) REVERT: B 635 TYR cc_start: 0.7499 (t80) cc_final: 0.7251 (t80) outliers start: 6 outliers final: 4 residues processed: 100 average time/residue: 1.5021 time to fit residues: 162.5062 Evaluate side-chains 105 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 490 LYS 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 33 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6046 Z= 0.210 Angle : 0.543 9.883 8238 Z= 0.272 Chirality : 0.084 1.700 990 Planarity : 0.004 0.039 994 Dihedral : 4.254 27.078 804 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.94 % Allowed : 12.07 % Favored : 86.99 % 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: 1.41 (0.31), residues: 746 helix: 1.43 (0.22), residues: 548 sheet: 1.86 (0.79), residues: 42 loop : -0.99 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 506 HIS 0.004 0.001 HIS A 57 PHE 0.018 0.001 PHE A 92 TYR 0.014 0.001 TYR B 635 ARG 0.003 0.000 ARG A 44 ********************** 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 fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ASN cc_start: 0.8330 (t0) cc_final: 0.7982 (t0) REVERT: A 635 TYR cc_start: 0.6777 (t80) cc_final: 0.6513 (t80) REVERT: B 473 MET cc_start: 0.4639 (OUTLIER) cc_final: 0.4179 (ptm) REVERT: B 608 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: B 610 ASN cc_start: 0.8285 (t0) cc_final: 0.7918 (t0) outliers start: 6 outliers final: 2 residues processed: 101 average time/residue: 1.5025 time to fit residues: 164.1645 Evaluate side-chains 104 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 473 MET 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 54 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 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 = 0.3854 r_free = 0.3854 target = 0.160529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136006 restraints weight = 21411.804| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.58 r_work: 0.3489 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6046 Z= 0.185 Angle : 0.545 9.910 8238 Z= 0.270 Chirality : 0.084 1.697 990 Planarity : 0.004 0.039 994 Dihedral : 4.217 26.356 804 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.94 % Allowed : 12.38 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.31), residues: 746 helix: 1.42 (0.22), residues: 550 sheet: 1.94 (0.79), residues: 42 loop : -0.86 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 506 HIS 0.003 0.000 HIS B 57 PHE 0.022 0.001 PHE B 92 TYR 0.009 0.001 TYR A 635 ARG 0.002 0.000 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4262.45 seconds wall clock time: 74 minutes 49.67 seconds (4489.67 seconds total)