Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:36:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/11_2022/7swp_25478_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/11_2022/7swp_25478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/11_2022/7swp_25478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/11_2022/7swp_25478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/11_2022/7swp_25478_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/11_2022/7swp_25478_neut.pdb" } resolution = 3.8 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= 0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 34": "OD1" <-> "OD2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3372 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1545 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1017 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 810 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.15, per 1000 atoms: 0.64 Number of scatterers: 3372 At special positions: 0 Unit cell: (84.15, 59.4, 89.1, 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 14 16.00 O 648 8.00 N 573 7.00 C 2137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 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: 1.37 Conformation dependent library (CDL) restraints added in 494.9 milliseconds 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 15.1% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.584A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.236A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.828A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.876A pdb=" N TYR H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.782A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.547A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.687A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.623A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 17 through 23 119 hydrogen bonds defined for protein. 273 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: 0.89 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1087 1.34 - 1.46: 924 1.46 - 1.58: 1434 1.58 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3461 Sorted by residual: bond pdb=" C TYR A 421 " pdb=" N ASN A 422 " ideal model delta sigma weight residual 1.332 1.282 0.050 1.40e-02 5.10e+03 1.27e+01 bond pdb=" C LYS A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 1.331 1.233 0.098 2.83e-02 1.25e+03 1.19e+01 bond pdb=" N VAL L 100 " pdb=" CA VAL L 100 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.21e-02 6.83e+03 8.88e+00 bond pdb=" N VAL L 101 " pdb=" CA VAL L 101 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.24e-02 6.50e+03 8.21e+00 bond pdb=" N THR L 106 " pdb=" CA THR L 106 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.96e+00 ... (remaining 3456 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.86: 113 106.86 - 113.65: 1798 113.65 - 120.43: 1310 120.43 - 127.21: 1450 127.21 - 133.99: 36 Bond angle restraints: 4707 Sorted by residual: angle pdb=" C HIS L 36 " pdb=" N TRP L 37 " pdb=" CA TRP L 37 " ideal model delta sigma weight residual 122.94 115.73 7.21 1.50e+00 4.44e-01 2.31e+01 angle pdb=" C TYR A 421 " pdb=" N ASN A 422 " pdb=" CA ASN A 422 " ideal model delta sigma weight residual 121.54 113.51 8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C PRO A 527 " pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 121.70 127.24 -5.54 1.80e+00 3.09e-01 9.48e+00 angle pdb=" N GLY A 526 " pdb=" CA GLY A 526 " pdb=" C GLY A 526 " ideal model delta sigma weight residual 112.34 118.59 -6.25 2.04e+00 2.40e-01 9.38e+00 angle pdb=" CA GLY L 103 " pdb=" C GLY L 103 " pdb=" O GLY L 103 " ideal model delta sigma weight residual 122.24 118.32 3.92 1.30e+00 5.92e-01 9.10e+00 ... (remaining 4702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 1840 17.57 - 35.15: 163 35.15 - 52.72: 15 52.72 - 70.29: 4 70.29 - 87.87: 2 Dihedral angle restraints: 2024 sinusoidal: 776 harmonic: 1248 Sorted by residual: dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 46.90 46.10 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CA SER A 477 " pdb=" C SER A 477 " pdb=" N THR A 478 " pdb=" CA THR A 478 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 2021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 354 0.048 - 0.096: 103 0.096 - 0.145: 33 0.145 - 0.193: 3 0.193 - 0.241: 2 Chirality restraints: 495 Sorted by residual: chirality pdb=" CB ILE L 50 " pdb=" CA ILE L 50 " pdb=" CG1 ILE L 50 " pdb=" CG2 ILE L 50 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU H 81 " pdb=" CB LEU H 81 " pdb=" CD1 LEU H 81 " pdb=" CD2 LEU H 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL L 101 " pdb=" N VAL L 101 " pdb=" C VAL L 101 " pdb=" CB VAL L 101 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 492 not shown) Planarity restraints: 617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 37 " -0.035 2.00e-02 2.50e+03 4.40e-02 4.85e+01 pdb=" CG TRP L 37 " 0.109 2.00e-02 2.50e+03 pdb=" CD1 TRP L 37 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP L 37 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP L 37 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP L 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP L 37 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 37 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 37 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP L 37 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 527 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 453 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C TYR A 453 " -0.025 2.00e-02 2.50e+03 pdb=" O TYR A 453 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG A 454 " 0.009 2.00e-02 2.50e+03 ... (remaining 614 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 569 2.74 - 3.28: 3775 3.28 - 3.82: 6048 3.82 - 4.36: 7001 4.36 - 4.90: 11348 Nonbonded interactions: 28741 Sorted by model distance: nonbonded pdb=" OD2 ASP L 94 " pdb=" OG SER L 96 " model vdw 2.202 2.440 nonbonded pdb=" NE2 GLN H 13 " pdb=" O SER H 128 " model vdw 2.206 2.520 nonbonded pdb=" O TYR H 53 " pdb=" NH2 ARG H 72 " model vdw 2.214 2.520 nonbonded pdb=" OG1 THR A 415 " pdb=" OG SER L 58 " model vdw 2.216 2.440 nonbonded pdb=" O LYS A 444 " pdb=" NE2 GLN A 498 " model vdw 2.224 2.520 ... (remaining 28736 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2137 2.51 5 N 573 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 3.070 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 13.740 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.008 0.098 3461 Z= 0.534 Angle : 0.925 8.029 4707 Z= 0.525 Chirality : 0.051 0.241 495 Planarity : 0.006 0.056 617 Dihedral : 12.869 87.868 1224 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 40.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % 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: -2.17 (0.38), residues: 430 helix: -3.11 (0.87), residues: 21 sheet: -1.11 (0.44), residues: 122 loop : -1.50 (0.36), residues: 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1898 time to fit residues: 35.6798 Evaluate side-chains 93 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3461 Z= 0.265 Angle : 0.781 9.014 4707 Z= 0.401 Chirality : 0.049 0.141 495 Planarity : 0.006 0.041 617 Dihedral : 5.823 25.181 487 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 3.57 % 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: -1.89 (0.37), residues: 430 helix: -3.44 (0.68), residues: 22 sheet: -0.92 (0.42), residues: 132 loop : -1.25 (0.35), residues: 276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.436 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 125 average time/residue: 0.1459 time to fit residues: 22.4646 Evaluate side-chains 109 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0365 time to fit residues: 1.0906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 3461 Z= 0.371 Angle : 0.785 6.826 4707 Z= 0.413 Chirality : 0.048 0.141 495 Planarity : 0.006 0.052 617 Dihedral : 5.801 26.849 487 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 25.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer Outliers : 4.67 % 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: -1.88 (0.37), residues: 430 helix: -3.43 (0.64), residues: 22 sheet: -0.84 (0.43), residues: 123 loop : -1.27 (0.34), residues: 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 115 average time/residue: 0.1405 time to fit residues: 19.9605 Evaluate side-chains 115 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0743 time to fit residues: 1.7491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3461 Z= 0.222 Angle : 0.720 8.181 4707 Z= 0.371 Chirality : 0.047 0.164 495 Planarity : 0.005 0.042 617 Dihedral : 5.354 24.081 487 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 2.75 % 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: -1.64 (0.38), residues: 430 helix: -3.47 (0.73), residues: 22 sheet: -0.85 (0.43), residues: 124 loop : -1.00 (0.36), residues: 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 120 average time/residue: 0.1482 time to fit residues: 21.6157 Evaluate side-chains 114 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0353 time to fit residues: 0.9776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 0.0770 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 3461 Z= 0.335 Angle : 0.778 8.390 4707 Z= 0.404 Chirality : 0.048 0.155 495 Planarity : 0.005 0.051 617 Dihedral : 5.650 24.058 487 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer Outliers : 5.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.39), residues: 430 helix: -3.56 (0.68), residues: 22 sheet: -0.57 (0.43), residues: 132 loop : -0.91 (0.37), residues: 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 123 average time/residue: 0.1336 time to fit residues: 20.3997 Evaluate side-chains 121 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0372 time to fit residues: 1.4894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 0.0010 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3461 Z= 0.207 Angle : 0.724 8.508 4707 Z= 0.371 Chirality : 0.047 0.167 495 Planarity : 0.005 0.040 617 Dihedral : 5.202 24.419 487 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 3.57 % 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: -1.31 (0.40), residues: 430 helix: -3.87 (0.57), residues: 22 sheet: -0.39 (0.44), residues: 131 loop : -0.83 (0.38), residues: 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 123 average time/residue: 0.1343 time to fit residues: 20.5070 Evaluate side-chains 120 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0377 time to fit residues: 1.2396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3461 Z= 0.218 Angle : 0.750 12.222 4707 Z= 0.376 Chirality : 0.047 0.171 495 Planarity : 0.005 0.041 617 Dihedral : 5.062 24.796 487 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 1.92 % 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: -1.22 (0.40), residues: 430 helix: -3.89 (0.57), residues: 22 sheet: -0.27 (0.44), residues: 131 loop : -0.80 (0.38), residues: 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 116 average time/residue: 0.1349 time to fit residues: 19.4361 Evaluate side-chains 111 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0410 time to fit residues: 0.9355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 3461 Z= 0.248 Angle : 0.748 13.218 4707 Z= 0.379 Chirality : 0.048 0.166 495 Planarity : 0.005 0.043 617 Dihedral : 5.039 24.879 487 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 25.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 2.75 % 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: -1.27 (0.40), residues: 430 helix: -3.72 (0.61), residues: 28 sheet: -0.14 (0.45), residues: 131 loop : -0.86 (0.38), residues: 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 111 average time/residue: 0.1372 time to fit residues: 18.9049 Evaluate side-chains 114 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.405 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0374 time to fit residues: 1.1838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 3461 Z= 0.268 Angle : 0.790 17.447 4707 Z= 0.399 Chirality : 0.048 0.168 495 Planarity : 0.005 0.047 617 Dihedral : 5.089 26.052 487 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 27.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 0.55 % 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: -1.39 (0.39), residues: 430 helix: -3.65 (0.60), residues: 28 sheet: -0.14 (0.45), residues: 132 loop : -1.03 (0.37), residues: 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 105 average time/residue: 0.1405 time to fit residues: 18.2922 Evaluate side-chains 105 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0454 time to fit residues: 0.6586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3461 Z= 0.220 Angle : 0.807 15.985 4707 Z= 0.400 Chirality : 0.048 0.200 495 Planarity : 0.005 0.045 617 Dihedral : 4.890 24.616 487 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.40), residues: 430 helix: -3.66 (0.62), residues: 28 sheet: -0.31 (0.44), residues: 138 loop : -0.90 (0.38), residues: 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 111 average time/residue: 0.1476 time to fit residues: 20.2264 Evaluate side-chains 108 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0449 time to fit residues: 0.8318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 0.0050 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.118693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.102041 restraints weight = 9125.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105386 restraints weight = 4823.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.107608 restraints weight = 3129.070| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 3461 Z= 0.282 Angle : 0.839 15.341 4707 Z= 0.418 Chirality : 0.048 0.184 495 Planarity : 0.005 0.045 617 Dihedral : 5.061 22.825 487 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 27.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 1.65 % 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: -1.39 (0.40), residues: 430 helix: -3.49 (0.67), residues: 28 sheet: -0.13 (0.46), residues: 131 loop : -1.05 (0.37), residues: 271 =============================================================================== Job complete usr+sys time: 1139.87 seconds wall clock time: 22 minutes 3.09 seconds (1323.09 seconds total)