Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 00:56:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/04_2023/8drq_27681.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/04_2023/8drq_27681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/04_2023/8drq_27681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/04_2023/8drq_27681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/04_2023/8drq_27681.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/04_2023/8drq_27681.pdb" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.045 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 8 5.16 5 C 2135 2.51 5 N 583 2.21 5 O 595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 473": "OE1" <-> "OE2" Residue "E TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 519": "OE1" <-> "OE2" Residue "E GLU 520": "OE1" <-> "OE2" Residue "E ASP 538": "OD1" <-> "OD2" Residue "E ASP 620": "OD1" <-> "OD2" Residue "E GLU 760": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Time building chain proxies: 2.33, per 1000 atoms: 0.70 Number of scatterers: 3321 At special positions: 0 Unit cell: (75.456, 81.744, 78.6, 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 8 16.00 O 595 8.00 N 583 7.00 C 2135 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: 1.32 Conformation dependent library (CDL) restraints added in 505.3 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 31.4% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'E' and resid 402 through 411 Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 444 removed outlier: 3.790A pdb=" N PHE E 443 " --> pdb=" O PRO E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 removed outlier: 3.589A pdb=" N ILE E 465 " --> pdb=" O PRO E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 510 through 514 removed outlier: 4.056A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.702A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.788A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 638 removed outlier: 3.750A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 removed outlier: 3.525A pdb=" N LEU E 661 " --> pdb=" O ILE E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 684 removed outlier: 3.647A pdb=" N CYS E 684 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.953A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 707 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 730 removed outlier: 3.629A pdb=" N PHE E 728 " --> pdb=" O PRO E 724 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS E 730 " --> pdb=" O GLU E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 753 Processing helix chain 'E' and resid 771 through 776 removed outlier: 3.560A pdb=" N CYS E 776 " --> pdb=" O GLU E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 788 through 793 Processing helix chain 'E' and resid 795 through 808 Processing sheet with id=AA1, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.410A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 474 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LYS E 501 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU E 476 " --> pdb=" O LYS E 501 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU E 498 " --> pdb=" O HIS E 522 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E 524 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE E 500 " --> pdb=" O THR E 524 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 596 " --> pdb=" O GLU E 618 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP E 620 " --> pdb=" O LEU E 596 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 598 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.483A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 666 through 668 removed outlier: 6.334A pdb=" N TYR E 689 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 159 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: 0.91 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1098 1.34 - 1.46: 490 1.46 - 1.58: 1779 1.58 - 1.69: 1 1.69 - 1.81: 10 Bond restraints: 3378 Sorted by residual: bond pdb=" N PRO E 678 " pdb=" CD PRO E 678 " ideal model delta sigma weight residual 1.473 1.417 0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" CB PRO E 678 " pdb=" CG PRO E 678 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.92e+00 bond pdb=" CB ASN E 712 " pdb=" CG ASN E 712 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.36e+00 bond pdb=" CG PRO E 678 " pdb=" CD PRO E 678 " ideal model delta sigma weight residual 1.503 1.460 0.043 3.40e-02 8.65e+02 1.57e+00 bond pdb=" N TYR E 534 " pdb=" CA TYR E 534 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.15e-02 7.56e+03 1.15e+00 ... (remaining 3373 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.36: 114 107.36 - 114.03: 1986 114.03 - 120.70: 1286 120.70 - 127.37: 1160 127.37 - 134.03: 34 Bond angle restraints: 4580 Sorted by residual: angle pdb=" CA MET E 590 " pdb=" CB MET E 590 " pdb=" CG MET E 590 " ideal model delta sigma weight residual 114.10 121.55 -7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB MET E 590 " pdb=" CG MET E 590 " pdb=" SD MET E 590 " ideal model delta sigma weight residual 112.70 122.86 -10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C ASN E 712 " pdb=" CA ASN E 712 " pdb=" CB ASN E 712 " ideal model delta sigma weight residual 109.38 115.03 -5.65 1.80e+00 3.09e-01 9.85e+00 angle pdb=" N PRO E 678 " pdb=" CD PRO E 678 " pdb=" CG PRO E 678 " ideal model delta sigma weight residual 103.20 107.80 -4.60 1.50e+00 4.44e-01 9.42e+00 angle pdb=" C LEU E 603 " pdb=" N GLU E 604 " pdb=" CA GLU E 604 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.02e+00 ... (remaining 4575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 1759 15.43 - 30.85: 250 30.85 - 46.28: 67 46.28 - 61.70: 17 61.70 - 77.13: 1 Dihedral angle restraints: 2094 sinusoidal: 892 harmonic: 1202 Sorted by residual: dihedral pdb=" CA LEU E 468 " pdb=" C LEU E 468 " pdb=" N THR E 469 " pdb=" CA THR E 469 " ideal model delta harmonic sigma weight residual 180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ILE E 535 " pdb=" C ILE E 535 " pdb=" N VAL E 536 " pdb=" CA VAL E 536 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR E 662 " pdb=" C THR E 662 " pdb=" N ASN E 663 " pdb=" CA ASN E 663 " ideal model delta harmonic sigma weight residual -180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 316 0.036 - 0.071: 163 0.071 - 0.107: 53 0.107 - 0.143: 15 0.143 - 0.178: 2 Chirality restraints: 549 Sorted by residual: chirality pdb=" CB VAL E 786 " pdb=" CA VAL E 786 " pdb=" CG1 VAL E 786 " pdb=" CG2 VAL E 786 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA VAL E 786 " pdb=" N VAL E 786 " pdb=" C VAL E 786 " pdb=" CB VAL E 786 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA ILE E 654 " pdb=" N ILE E 654 " pdb=" C ILE E 654 " pdb=" CB ILE E 654 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 546 not shown) Planarity restraints: 578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 677 " -0.047 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO E 678 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 678 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 678 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 490 " -0.007 2.00e-02 2.50e+03 1.84e-02 5.90e+00 pdb=" CG PHE E 490 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 490 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE E 490 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE E 490 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 490 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 490 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 746 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO E 747 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 747 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 747 " 0.026 5.00e-02 4.00e+02 ... (remaining 575 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 850 2.81 - 3.33: 3133 3.33 - 3.85: 5736 3.85 - 4.38: 7140 4.38 - 4.90: 11097 Nonbonded interactions: 27956 Sorted by model distance: nonbonded pdb=" O VAL E 591 " pdb=" ND2 ASN E 615 " model vdw 2.283 2.520 nonbonded pdb=" O LEU E 476 " pdb=" N LYS E 501 " model vdw 2.300 2.520 nonbonded pdb=" OH TYR E 689 " pdb=" OE1 GLN E 711 " model vdw 2.315 2.440 nonbonded pdb=" O GLN E 560 " pdb=" OG1 THR E 563 " model vdw 2.328 2.440 nonbonded pdb=" O LEU E 790 " pdb=" OG1 THR E 793 " model vdw 2.329 2.440 ... (remaining 27951 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 14.660 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.150 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 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 0.122 3378 Z= 0.295 Angle : 0.891 10.159 4580 Z= 0.486 Chirality : 0.048 0.178 549 Planarity : 0.006 0.073 578 Dihedral : 15.597 77.126 1306 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.00 % 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: -3.30 (0.39), residues: 405 helix: -3.27 (0.37), residues: 114 sheet: -2.33 (0.78), residues: 54 loop : -1.55 (0.38), residues: 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2430 time to fit residues: 39.2052 Evaluate side-chains 95 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 0.0670 chunk 36 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 614 HIS E 711 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3378 Z= 0.195 Angle : 0.709 7.359 4580 Z= 0.344 Chirality : 0.047 0.163 549 Planarity : 0.005 0.049 578 Dihedral : 5.558 18.993 439 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 23.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.00 % 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: -3.51 (0.38), residues: 405 helix: -2.86 (0.37), residues: 134 sheet: -2.32 (0.76), residues: 52 loop : -1.93 (0.39), residues: 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2244 time to fit residues: 28.0921 Evaluate side-chains 78 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 0.0970 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 614 HIS E 694 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5814 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3378 Z= 0.175 Angle : 0.653 7.684 4580 Z= 0.319 Chirality : 0.044 0.143 549 Planarity : 0.005 0.065 578 Dihedral : 5.119 17.928 439 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.00 % 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: -3.33 (0.39), residues: 405 helix: -2.67 (0.39), residues: 134 sheet: -1.96 (0.77), residues: 48 loop : -1.94 (0.40), residues: 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1984 time to fit residues: 23.3813 Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 ASN E 711 GLN E 729 GLN E 755 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.6778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 3378 Z= 0.314 Angle : 0.873 9.855 4580 Z= 0.415 Chirality : 0.050 0.217 549 Planarity : 0.006 0.057 578 Dihedral : 6.059 20.623 439 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 0.00 % 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: -3.70 (0.37), residues: 405 helix: -2.97 (0.36), residues: 130 sheet: -1.73 (0.80), residues: 43 loop : -2.32 (0.37), residues: 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2023 time to fit residues: 21.8435 Evaluate side-chains 72 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 694 HIS E 755 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.7379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3378 Z= 0.207 Angle : 0.695 8.631 4580 Z= 0.335 Chirality : 0.046 0.150 549 Planarity : 0.005 0.055 578 Dihedral : 5.487 17.748 439 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer Outliers : 0.00 % 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: -3.43 (0.38), residues: 405 helix: -2.43 (0.41), residues: 130 sheet: -1.79 (0.79), residues: 43 loop : -2.32 (0.38), residues: 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2076 time to fit residues: 22.5841 Evaluate side-chains 72 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 625 ASN ** E 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.7882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3378 Z= 0.196 Angle : 0.685 6.555 4580 Z= 0.338 Chirality : 0.047 0.169 549 Planarity : 0.005 0.042 578 Dihedral : 5.381 16.556 439 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer Outliers : 0.00 % 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: -2.73 (0.40), residues: 405 helix: -2.05 (0.48), residues: 105 sheet: -1.78 (0.79), residues: 44 loop : -1.75 (0.38), residues: 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2215 time to fit residues: 22.7487 Evaluate side-chains 69 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 554 ASN E 625 ASN ** E 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.8441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3378 Z= 0.222 Angle : 0.737 6.647 4580 Z= 0.364 Chirality : 0.048 0.151 549 Planarity : 0.005 0.053 578 Dihedral : 5.629 16.257 439 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 0.26 % 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 (0.40), residues: 405 helix: -2.28 (0.47), residues: 104 sheet: -1.92 (0.78), residues: 45 loop : -1.75 (0.38), residues: 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1792 time to fit residues: 17.5008 Evaluate side-chains 62 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 ASN E 554 ASN E 625 ASN E 708 GLN ** E 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.9277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 3378 Z= 0.324 Angle : 0.903 8.896 4580 Z= 0.449 Chirality : 0.053 0.188 549 Planarity : 0.006 0.045 578 Dihedral : 6.571 22.534 439 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 33.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer Outliers : 0.00 % 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: -3.36 (0.39), residues: 405 helix: -2.85 (0.43), residues: 110 sheet: -2.07 (0.78), residues: 47 loop : -2.01 (0.38), residues: 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1906 time to fit residues: 18.3309 Evaluate side-chains 57 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 chunk 3 optimal weight: 0.0270 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 ASN E 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.9333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 3378 Z= 0.190 Angle : 0.723 6.998 4580 Z= 0.354 Chirality : 0.047 0.140 549 Planarity : 0.005 0.042 578 Dihedral : 5.449 18.155 439 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer Outliers : 0.00 % 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: -3.32 (0.38), residues: 405 helix: -2.71 (0.42), residues: 118 sheet: -1.54 (0.80), residues: 44 loop : -2.12 (0.37), residues: 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1667 time to fit residues: 17.3769 Evaluate side-chains 62 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN E 709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.9641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 3378 Z= 0.218 Angle : 0.743 6.715 4580 Z= 0.366 Chirality : 0.048 0.151 549 Planarity : 0.005 0.055 578 Dihedral : 5.582 18.611 439 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer Outliers : 0.00 % 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: -3.32 (0.39), residues: 405 helix: -2.75 (0.42), residues: 118 sheet: -1.49 (0.82), residues: 45 loop : -2.10 (0.38), residues: 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1793 time to fit residues: 17.7434 Evaluate side-chains 62 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.0010 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 0.0040 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 532 ASN E 625 ASN E 709 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.138191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.127273 restraints weight = 17795.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.128716 restraints weight = 12901.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.129922 restraints weight = 9712.358| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 moved from start: 0.9709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3378 Z= 0.187 Angle : 0.689 7.106 4580 Z= 0.330 Chirality : 0.046 0.134 549 Planarity : 0.005 0.037 578 Dihedral : 5.032 15.185 439 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 0.00 % 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: -3.21 (0.39), residues: 405 helix: -2.60 (0.43), residues: 118 sheet: -1.49 (0.79), residues: 45 loop : -2.05 (0.38), residues: 242 =============================================================================== Job complete usr+sys time: 1490.37 seconds wall clock time: 27 minutes 18.91 seconds (1638.91 seconds total)