Starting phenix.real_space_refine on Sun Mar 10 15:27:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/03_2024/7n5g_24189_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/03_2024/7n5g_24189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/03_2024/7n5g_24189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/03_2024/7n5g_24189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/03_2024/7n5g_24189_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/03_2024/7n5g_24189_updated.pdb" } resolution = 2.4 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1920 2.51 5 N 486 2.21 5 O 508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2926 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2926 Unusual residues: {'PLM': 1} Classifications: {'peptide': 371, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363, None: 1} Not linked: pdbres="ASN B 751 " pdbres="PLM B 801 " Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Time building chain proxies: 2.13, per 1000 atoms: 0.73 Number of scatterers: 2926 At special positions: 0 Unit cell: (70.04, 93.73, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 508 8.00 N 486 7.00 C 1920 6.00 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: 1.14 Conformation dependent library (CDL) restraints added in 520.9 milliseconds 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 2 sheets defined 60.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 265 through 284 Processing helix chain 'B' and resid 296 through 330 removed outlier: 3.905A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 350 removed outlier: 5.033A pdb=" N ASP B 337 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 349 " --> pdb=" O HIS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 551 removed outlier: 4.134A pdb=" N ASN B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL B 529 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 589 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 4.664A pdb=" N THR B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 677 Processing helix chain 'B' and resid 715 through 735 Processing sheet with id= A, first strand: chain 'B' and resid 639 through 641 removed outlier: 6.842A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.749A pdb=" N ALA B 703 " --> pdb=" O VAL B 691 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL B 691 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE B 705 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET B 689 " --> pdb=" O PHE B 705 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 675 1.32 - 1.44: 718 1.44 - 1.57: 1550 1.57 - 1.69: 16 1.69 - 1.81: 21 Bond restraints: 2980 Sorted by residual: bond pdb=" CD2 TRP B 507 " pdb=" CE3 TRP B 507 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.27e+01 bond pdb=" CZ2 TRP B 507 " pdb=" CH2 TRP B 507 " ideal model delta sigma weight residual 1.368 1.480 -0.112 1.90e-02 2.77e+03 3.46e+01 bond pdb=" CB ILE B 285 " pdb=" CG1 ILE B 285 " ideal model delta sigma weight residual 1.530 1.635 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" CB TYR B 629 " pdb=" CG TYR B 629 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.65e+01 bond pdb=" CB HIS B 345 " pdb=" CG HIS B 345 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.46e+01 ... (remaining 2975 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.94: 53 105.94 - 113.05: 1626 113.05 - 120.16: 1256 120.16 - 127.27: 1072 127.27 - 134.38: 32 Bond angle restraints: 4039 Sorted by residual: angle pdb=" C HIS B 592 " pdb=" N PRO B 593 " pdb=" CA PRO B 593 " ideal model delta sigma weight residual 119.56 126.54 -6.98 1.01e+00 9.80e-01 4.78e+01 angle pdb=" C SER B 645 " pdb=" N PRO B 646 " pdb=" CA PRO B 646 " ideal model delta sigma weight residual 120.52 126.91 -6.39 9.90e-01 1.02e+00 4.17e+01 angle pdb=" C LEU B 743 " pdb=" N PRO B 744 " pdb=" CA PRO B 744 " ideal model delta sigma weight residual 119.85 126.24 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C GLN B 291 " pdb=" N PRO B 292 " pdb=" CA PRO B 292 " ideal model delta sigma weight residual 119.28 125.41 -6.13 1.10e+00 8.26e-01 3.11e+01 angle pdb=" N SER B 267 " pdb=" CA SER B 267 " pdb=" C SER B 267 " ideal model delta sigma weight residual 112.23 105.58 6.65 1.26e+00 6.30e-01 2.79e+01 ... (remaining 4034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 1685 14.33 - 28.65: 62 28.65 - 42.97: 7 42.97 - 57.30: 11 57.30 - 71.62: 6 Dihedral angle restraints: 1771 sinusoidal: 680 harmonic: 1091 Sorted by residual: dihedral pdb=" CA ASP B 657 " pdb=" CB ASP B 657 " pdb=" CG ASP B 657 " pdb=" OD1 ASP B 657 " ideal model delta sinusoidal sigma weight residual -30.00 -84.87 54.87 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP B 595 " pdb=" CB ASP B 595 " pdb=" CG ASP B 595 " pdb=" OD1 ASP B 595 " ideal model delta sinusoidal sigma weight residual -30.00 -74.43 44.43 1 2.00e+01 2.50e-03 6.86e+00 dihedral pdb=" N ASP B 650 " pdb=" C ASP B 650 " pdb=" CA ASP B 650 " pdb=" CB ASP B 650 " ideal model delta harmonic sigma weight residual 122.80 116.39 6.41 0 2.50e+00 1.60e-01 6.57e+00 ... (remaining 1768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 371 0.097 - 0.193: 99 0.193 - 0.290: 16 0.290 - 0.387: 3 0.387 - 0.483: 2 Chirality restraints: 491 Sorted by residual: chirality pdb=" CG LEU B 264 " pdb=" CB LEU B 264 " pdb=" CD1 LEU B 264 " pdb=" CD2 LEU B 264 " both_signs ideal model delta sigma weight residual False -2.59 -3.07 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CB ILE B 285 " pdb=" CA ILE B 285 " pdb=" CG1 ILE B 285 " pdb=" CG2 ILE B 285 " both_signs ideal model delta sigma weight residual False 2.64 3.05 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA TRP B 304 " pdb=" N TRP B 304 " pdb=" C TRP B 304 " pdb=" CB TRP B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 488 not shown) Planarity restraints: 493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 697 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C VAL B 697 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL B 697 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN B 698 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 675 " 0.035 2.00e-02 2.50e+03 1.98e-02 7.85e+00 pdb=" CG TYR B 675 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 675 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 675 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 675 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 675 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 675 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 675 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 741 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C ASN B 741 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN B 741 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 742 " -0.014 2.00e-02 2.50e+03 ... (remaining 490 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1129 2.89 - 3.39: 3007 3.39 - 3.89: 4769 3.89 - 4.40: 5456 4.40 - 4.90: 8449 Nonbonded interactions: 22810 Sorted by model distance: nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 2.520 nonbonded pdb=" N VAL B 697 " pdb=" N ASN B 698 " model vdw 2.467 2.560 nonbonded pdb=" N ASN B 711 " pdb=" O ASN B 711 " model vdw 2.498 2.496 nonbonded pdb=" N PRO B 646 " pdb=" O PRO B 646 " model vdw 2.533 2.496 nonbonded pdb=" N ASN B 613 " pdb=" O ASN B 613 " model vdw 2.553 2.496 ... (remaining 22805 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.410 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.970 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.022 0.132 2980 Z= 1.475 Angle : 1.511 8.243 4039 Z= 1.034 Chirality : 0.093 0.483 491 Planarity : 0.008 0.031 493 Dihedral : 10.569 71.622 1051 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.84 (0.41), residues: 361 helix: 1.41 (0.30), residues: 223 sheet: 0.94 (0.88), residues: 42 loop : 1.21 (0.65), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.008 TRP B 683 HIS 0.005 0.002 HIS B 346 PHE 0.019 0.005 PHE B 682 TYR 0.035 0.008 TYR B 675 ARG 0.005 0.001 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 526 LYS cc_start: 0.7984 (mttt) cc_final: 0.7595 (mtpp) REVERT: B 624 LYS cc_start: 0.8434 (mmtm) cc_final: 0.7572 (tttp) REVERT: B 702 MET cc_start: 0.8860 (mtt) cc_final: 0.8638 (mtp) outliers start: 0 outliers final: 1 residues processed: 99 average time/residue: 1.1619 time to fit residues: 117.8353 Evaluate side-chains 85 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 560 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 605 ASN B 648 GLN B 688 ASN B 698 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2980 Z= 0.190 Angle : 0.501 6.069 4039 Z= 0.274 Chirality : 0.041 0.136 491 Planarity : 0.004 0.038 493 Dihedral : 8.449 54.927 397 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.56 % Allowed : 9.12 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.43), residues: 361 helix: 2.20 (0.32), residues: 228 sheet: 0.70 (0.80), residues: 42 loop : 0.70 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 281 HIS 0.004 0.001 HIS B 592 PHE 0.011 0.002 PHE B 271 TYR 0.006 0.001 TYR B 629 ARG 0.004 0.001 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: B 301 PHE cc_start: 0.7218 (t80) cc_final: 0.6989 (t80) outliers start: 14 outliers final: 7 residues processed: 95 average time/residue: 1.1436 time to fit residues: 111.3816 Evaluate side-chains 94 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2980 Z= 0.198 Angle : 0.463 6.592 4039 Z= 0.248 Chirality : 0.040 0.132 491 Planarity : 0.003 0.018 493 Dihedral : 8.082 58.481 397 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.23 % Allowed : 10.75 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.44), residues: 361 helix: 2.42 (0.33), residues: 228 sheet: 0.77 (0.76), residues: 42 loop : 0.47 (0.68), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 316 HIS 0.004 0.001 HIS B 708 PHE 0.011 0.002 PHE B 271 TYR 0.008 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 624 LYS cc_start: 0.8421 (mmtm) cc_final: 0.7840 (tmmt) outliers start: 13 outliers final: 6 residues processed: 90 average time/residue: 1.1802 time to fit residues: 108.8681 Evaluate side-chains 87 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2980 Z= 0.195 Angle : 0.459 6.885 4039 Z= 0.242 Chirality : 0.040 0.137 491 Planarity : 0.003 0.019 493 Dihedral : 7.544 57.031 395 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.58 % Allowed : 14.98 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.44), residues: 361 helix: 2.61 (0.33), residues: 228 sheet: 0.81 (0.77), residues: 42 loop : 0.22 (0.68), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.011 0.001 PHE B 271 TYR 0.008 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 316 TRP cc_start: 0.8290 (t-100) cc_final: 0.8023 (t-100) REVERT: B 624 LYS cc_start: 0.8449 (mmtm) cc_final: 0.7937 (tmmt) outliers start: 11 outliers final: 5 residues processed: 88 average time/residue: 1.1750 time to fit residues: 105.9267 Evaluate side-chains 90 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2980 Z= 0.181 Angle : 0.440 7.035 4039 Z= 0.230 Chirality : 0.039 0.134 491 Planarity : 0.003 0.017 493 Dihedral : 7.458 59.409 395 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.61 % Allowed : 16.29 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.44), residues: 361 helix: 2.72 (0.33), residues: 228 sheet: 0.70 (0.76), residues: 42 loop : 0.11 (0.68), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.010 0.001 PHE B 271 TYR 0.007 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: B 316 TRP cc_start: 0.8266 (t-100) cc_final: 0.8010 (t-100) REVERT: B 624 LYS cc_start: 0.8483 (mmtm) cc_final: 0.8016 (tmmt) outliers start: 8 outliers final: 4 residues processed: 89 average time/residue: 1.1691 time to fit residues: 106.5860 Evaluate side-chains 88 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2980 Z= 0.218 Angle : 0.460 7.164 4039 Z= 0.238 Chirality : 0.040 0.126 491 Planarity : 0.003 0.019 493 Dihedral : 7.249 55.536 395 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.93 % Allowed : 15.64 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.45), residues: 361 helix: 2.71 (0.34), residues: 228 sheet: 0.45 (0.75), residues: 42 loop : 0.10 (0.69), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.011 0.001 PHE B 271 TYR 0.008 0.001 TYR B 740 ARG 0.002 0.000 ARG B 722 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: B 316 TRP cc_start: 0.8282 (t-100) cc_final: 0.8005 (t-100) REVERT: B 624 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8027 (tmmt) outliers start: 9 outliers final: 7 residues processed: 91 average time/residue: 1.1473 time to fit residues: 107.0675 Evaluate side-chains 93 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.0470 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2980 Z= 0.154 Angle : 0.430 7.684 4039 Z= 0.223 Chirality : 0.039 0.131 491 Planarity : 0.003 0.015 493 Dihedral : 7.075 54.341 395 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.28 % Allowed : 16.29 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.45), residues: 361 helix: 2.82 (0.34), residues: 228 sheet: 0.37 (0.74), residues: 42 loop : 0.14 (0.70), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 PHE 0.011 0.001 PHE B 654 TYR 0.006 0.001 TYR B 740 ARG 0.001 0.000 ARG B 722 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: B 624 LYS cc_start: 0.8472 (mmtm) cc_final: 0.8027 (tmmt) outliers start: 7 outliers final: 3 residues processed: 88 average time/residue: 1.1887 time to fit residues: 107.2095 Evaluate side-chains 89 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2980 Z= 0.172 Angle : 0.440 8.190 4039 Z= 0.225 Chirality : 0.039 0.128 491 Planarity : 0.003 0.016 493 Dihedral : 6.969 50.459 395 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.95 % Allowed : 16.94 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.45), residues: 361 helix: 2.84 (0.34), residues: 228 sheet: 0.35 (0.75), residues: 42 loop : 0.11 (0.70), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 PHE 0.010 0.001 PHE B 654 TYR 0.007 0.001 TYR B 740 ARG 0.001 0.000 ARG B 671 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: B 624 LYS cc_start: 0.8471 (mmtm) cc_final: 0.8036 (tmmt) outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 1.1431 time to fit residues: 104.2620 Evaluate side-chains 91 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.0770 chunk 10 optimal weight: 0.0030 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.3148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 515 GLN B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2980 Z= 0.117 Angle : 0.426 9.226 4039 Z= 0.215 Chirality : 0.038 0.132 491 Planarity : 0.002 0.015 493 Dihedral : 6.870 48.916 395 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.95 % Allowed : 16.61 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.45), residues: 361 helix: 2.98 (0.33), residues: 228 sheet: 0.36 (0.77), residues: 37 loop : 0.16 (0.68), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 548 HIS 0.002 0.000 HIS B 708 PHE 0.010 0.001 PHE B 572 TYR 0.006 0.001 TYR B 740 ARG 0.001 0.000 ARG B 722 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: B 624 LYS cc_start: 0.8459 (mmtm) cc_final: 0.8032 (tmmt) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 1.1850 time to fit residues: 109.3334 Evaluate side-chains 92 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2980 Z= 0.121 Angle : 0.438 9.814 4039 Z= 0.219 Chirality : 0.038 0.133 491 Planarity : 0.002 0.015 493 Dihedral : 6.778 44.001 395 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.63 % Allowed : 18.24 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.45), residues: 361 helix: 3.09 (0.33), residues: 228 sheet: 0.26 (0.77), residues: 37 loop : 0.15 (0.67), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 548 HIS 0.002 0.000 HIS B 708 PHE 0.009 0.001 PHE B 654 TYR 0.005 0.001 TYR B 740 ARG 0.002 0.000 ARG B 599 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 294 GLN cc_start: 0.7105 (tt0) cc_final: 0.6276 (pm20) REVERT: B 624 LYS cc_start: 0.8449 (mmtm) cc_final: 0.8034 (tmmt) outliers start: 5 outliers final: 5 residues processed: 90 average time/residue: 1.1915 time to fit residues: 109.8282 Evaluate side-chains 94 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 0.0050 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.161294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.136302 restraints weight = 3947.501| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.85 r_work: 0.3726 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2980 Z= 0.155 Angle : 0.449 10.117 4039 Z= 0.225 Chirality : 0.039 0.129 491 Planarity : 0.002 0.014 493 Dihedral : 6.707 44.194 395 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.30 % Allowed : 18.57 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.45), residues: 361 helix: 3.13 (0.34), residues: 228 sheet: 0.23 (0.77), residues: 37 loop : 0.12 (0.67), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 PHE 0.010 0.001 PHE B 654 TYR 0.007 0.001 TYR B 740 ARG 0.002 0.000 ARG B 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2349.07 seconds wall clock time: 41 minutes 51.75 seconds (2511.75 seconds total)