Starting phenix.real_space_refine (version: dev) on Fri Feb 17 04:02:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp1_32666/02_2023/7wp1_32666.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp1_32666/02_2023/7wp1_32666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp1_32666/02_2023/7wp1_32666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp1_32666/02_2023/7wp1_32666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp1_32666/02_2023/7wp1_32666.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp1_32666/02_2023/7wp1_32666.pdb" } resolution = 3.77 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= 0.009 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 Process input model Symmetric amino acids flipped Residue "L GLU 83": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 403": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 3305 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "F" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1464 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.63, per 1000 atoms: 0.80 Number of scatterers: 3305 At special positions: 0 Unit cell: (87.914, 63.018, 81.69, 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 15 16.00 O 643 8.00 N 551 7.00 C 2096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 565.6 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 7 sheets defined 4.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.536A pdb=" N GLY L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.853A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 410 removed outlier: 4.734A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.941A pdb=" N THR L 109 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY L 12 " --> pdb=" O THR L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.500A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.636A pdb=" N THR H 125 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR H 94 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 92 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 376 through 378 removed outlier: 3.575A pdb=" N THR F 376 " --> pdb=" O ALA F 435 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 435 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 452 through 454 57 hydrogen bonds defined for protein. 123 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: 0.73 Time building geometry restraints manager: 1.59 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: 1021 1.34 - 1.46: 851 1.46 - 1.58: 1498 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3389 Sorted by residual: bond pdb=" CB ASN F 370 " pdb=" CG ASN F 370 " ideal model delta sigma weight residual 1.516 1.575 -0.059 2.50e-02 1.60e+03 5.61e+00 bond pdb=" CA ASN F 370 " pdb=" CB ASN F 370 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.43e-02 4.89e+03 5.60e+00 bond pdb=" C LEU F 425 " pdb=" N PRO F 426 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.25e-02 6.40e+03 3.51e+00 bond pdb=" C GLY L 12 " pdb=" N ALA L 13 " ideal model delta sigma weight residual 1.330 1.304 0.026 1.47e-02 4.63e+03 3.23e+00 bond pdb=" CA CYS F 336 " pdb=" C CYS F 336 " ideal model delta sigma weight residual 1.525 1.562 -0.037 2.10e-02 2.27e+03 3.10e+00 ... (remaining 3384 not shown) Histogram of bond angle deviations from ideal: 98.98 - 105.99: 77 105.99 - 112.99: 1643 112.99 - 120.00: 1203 120.00 - 127.01: 1637 127.01 - 134.02: 43 Bond angle restraints: 4603 Sorted by residual: angle pdb=" N VAL F 367 " pdb=" CA VAL F 367 " pdb=" C VAL F 367 " ideal model delta sigma weight residual 113.47 107.26 6.21 1.01e+00 9.80e-01 3.78e+01 angle pdb=" N ILE F 468 " pdb=" CA ILE F 468 " pdb=" C ILE F 468 " ideal model delta sigma weight residual 112.12 107.84 4.28 8.40e-01 1.42e+00 2.60e+01 angle pdb=" CA ASN F 370 " pdb=" CB ASN F 370 " pdb=" CG ASN F 370 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" N CYS F 391 " pdb=" CA CYS F 391 " pdb=" C CYS F 391 " ideal model delta sigma weight residual 113.23 118.58 -5.35 1.22e+00 6.72e-01 1.92e+01 angle pdb=" C2 NAG A 1 " pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 109.64 111.95 -2.31 5.38e-01 3.45e+00 1.85e+01 ... (remaining 4598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 1731 17.43 - 34.86: 195 34.86 - 52.29: 30 52.29 - 69.72: 4 69.72 - 87.15: 2 Dihedral angle restraints: 1962 sinusoidal: 753 harmonic: 1209 Sorted by residual: dihedral pdb=" CA LEU F 390 " pdb=" C LEU F 390 " pdb=" N CYS F 391 " pdb=" CA CYS F 391 " ideal model delta harmonic sigma weight residual 180.00 145.06 34.94 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA ASP H 113 " pdb=" C ASP H 113 " pdb=" N TYR H 114 " pdb=" CA TYR H 114 " ideal model delta harmonic sigma weight residual -180.00 -146.69 -33.31 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CA TYR F 380 " pdb=" C TYR F 380 " pdb=" N GLY F 381 " pdb=" CA GLY F 381 " ideal model delta harmonic sigma weight residual 180.00 -148.09 -31.91 0 5.00e+00 4.00e-02 4.07e+01 ... (remaining 1959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 474 0.138 - 0.277: 15 0.277 - 0.415: 0 0.415 - 0.553: 0 0.553 - 0.691: 1 Chirality restraints: 490 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.18e+01 chirality pdb=" CA ASN F 370 " pdb=" N ASN F 370 " pdb=" C ASN F 370 " pdb=" CB ASN F 370 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 487 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.284 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" C7 NAG A 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.421 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.274 2.00e-02 2.50e+03 2.28e-01 6.52e+02 pdb=" C7 NAG A 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.384 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO H 14 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.036 5.00e-02 4.00e+02 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1171 2.85 - 3.36: 2769 3.36 - 3.88: 5198 3.88 - 4.39: 5643 4.39 - 4.90: 10286 Nonbonded interactions: 25067 Sorted by model distance: nonbonded pdb=" O SER F 366 " pdb=" OG SER F 366 " model vdw 2.338 2.440 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.345 2.440 nonbonded pdb=" NE2 HIS L 36 " pdb=" O ASN H 115 " model vdw 2.360 2.520 nonbonded pdb=" OG1 THR F 393 " pdb=" O GLU F 516 " model vdw 2.364 2.440 nonbonded pdb=" OH TYR L 38 " pdb=" OE1 GLN L 91 " model vdw 2.370 2.440 ... (remaining 25062 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 15 5.16 5 C 2096 2.51 5 N 551 2.21 5 O 643 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=0.00 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: 12.430 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: 45.020 Check model and map are aligned: 0.060 Process input model: 14.780 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 75.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.006 0.059 3389 Z= 0.368 Angle : 1.163 12.344 4603 Z= 0.693 Chirality : 0.068 0.691 490 Planarity : 0.016 0.243 595 Dihedral : 14.497 87.147 1197 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.23 % Favored : 87.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -5.40 (0.31), residues: 417 helix: -5.32 (0.22), residues: 20 sheet: -3.25 (0.37), residues: 145 loop : -3.79 (0.28), residues: 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2509 time to fit residues: 24.6618 Evaluate side-chains 67 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.3980 chunk 31 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN H 74 ASN H 115 ASN F 388 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 3389 Z= 0.310 Angle : 0.748 7.402 4603 Z= 0.403 Chirality : 0.053 0.526 490 Planarity : 0.006 0.052 595 Dihedral : 7.174 33.718 486 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.47 % Favored : 87.05 % Rotamer Outliers : 5.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.87 (0.35), residues: 417 helix: -5.29 (0.23), residues: 20 sheet: -2.85 (0.35), residues: 168 loop : -3.38 (0.34), residues: 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.444 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 84 average time/residue: 0.2224 time to fit residues: 21.6395 Evaluate side-chains 87 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0336 time to fit residues: 1.5295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 3389 Z= 0.361 Angle : 0.767 8.600 4603 Z= 0.410 Chirality : 0.054 0.499 490 Planarity : 0.006 0.050 595 Dihedral : 7.113 31.538 486 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.87 % Favored : 84.89 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.51 (0.37), residues: 417 helix: -5.28 (0.23), residues: 20 sheet: -2.63 (0.37), residues: 170 loop : -3.09 (0.37), residues: 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.394 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 79 average time/residue: 0.2441 time to fit residues: 21.8899 Evaluate side-chains 70 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0321 time to fit residues: 0.6245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0570 chunk 28 optimal weight: 0.0670 chunk 19 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3389 Z= 0.188 Angle : 0.674 8.354 4603 Z= 0.351 Chirality : 0.051 0.490 490 Planarity : 0.005 0.047 595 Dihedral : 6.344 30.660 486 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.75 % Favored : 88.01 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.30 (0.38), residues: 417 helix: -5.20 (0.26), residues: 21 sheet: -2.50 (0.37), residues: 171 loop : -2.91 (0.38), residues: 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.400 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 83 average time/residue: 0.2631 time to fit residues: 25.1089 Evaluate side-chains 81 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0366 time to fit residues: 1.2545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 3389 Z= 0.268 Angle : 0.718 8.105 4603 Z= 0.377 Chirality : 0.052 0.470 490 Planarity : 0.005 0.055 595 Dihedral : 6.375 28.057 486 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.71 % Favored : 87.05 % Rotamer Outliers : 3.97 % 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: -4.06 (0.38), residues: 417 helix: -5.18 (0.37), residues: 14 sheet: -2.50 (0.38), residues: 159 loop : -2.73 (0.37), residues: 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.398 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 79 average time/residue: 0.2248 time to fit residues: 20.6058 Evaluate side-chains 75 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0339 time to fit residues: 1.0582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 22 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 3389 Z= 0.336 Angle : 0.759 8.951 4603 Z= 0.402 Chirality : 0.053 0.475 490 Planarity : 0.006 0.059 595 Dihedral : 6.603 29.159 486 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.63 % Favored : 85.13 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.38), residues: 417 helix: -5.05 (0.36), residues: 19 sheet: -2.38 (0.38), residues: 162 loop : -2.72 (0.38), residues: 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.387 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.2307 time to fit residues: 17.5938 Evaluate side-chains 68 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0334 time to fit residues: 0.8461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN F 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 3389 Z= 0.249 Angle : 0.719 8.195 4603 Z= 0.379 Chirality : 0.051 0.471 490 Planarity : 0.005 0.046 595 Dihedral : 6.385 28.899 486 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.19 % Favored : 86.57 % Rotamer Outliers : 1.70 % 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: -4.00 (0.38), residues: 417 helix: -4.93 (0.43), residues: 19 sheet: -2.32 (0.39), residues: 164 loop : -2.74 (0.37), residues: 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.419 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 0.2343 time to fit residues: 18.7734 Evaluate side-chains 67 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0374 time to fit residues: 0.7093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.0370 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 3389 Z= 0.248 Angle : 0.710 7.610 4603 Z= 0.374 Chirality : 0.051 0.463 490 Planarity : 0.004 0.046 595 Dihedral : 6.334 27.388 486 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.15 % Favored : 85.61 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.38), residues: 417 helix: -4.81 (0.52), residues: 19 sheet: -2.31 (0.40), residues: 157 loop : -2.60 (0.37), residues: 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.404 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 66 average time/residue: 0.2322 time to fit residues: 17.8475 Evaluate side-chains 69 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0342 time to fit residues: 0.9399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.0170 chunk 38 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 27 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3389 Z= 0.202 Angle : 0.684 6.738 4603 Z= 0.358 Chirality : 0.050 0.452 490 Planarity : 0.004 0.046 595 Dihedral : 6.094 25.670 486 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.75 % Favored : 88.01 % Rotamer Outliers : 0.28 % 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: -3.84 (0.38), residues: 417 helix: -4.67 (0.63), residues: 19 sheet: -2.25 (0.40), residues: 160 loop : -2.61 (0.37), residues: 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.402 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.2334 time to fit residues: 18.0768 Evaluate side-chains 63 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 3389 Z= 0.401 Angle : 0.791 9.505 4603 Z= 0.416 Chirality : 0.054 0.460 490 Planarity : 0.005 0.044 595 Dihedral : 6.686 29.376 486 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.87 % Favored : 84.89 % Rotamer Outliers : 1.98 % 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: -3.86 (0.38), residues: 417 helix: -4.71 (0.62), residues: 19 sheet: -2.24 (0.40), residues: 161 loop : -2.64 (0.37), residues: 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.356 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 0.2259 time to fit residues: 17.8470 Evaluate side-chains 70 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0354 time to fit residues: 0.8877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132492 restraints weight = 5271.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135758 restraints weight = 3232.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138062 restraints weight = 2221.737| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 3389 Z= 0.334 Angle : 0.766 9.558 4603 Z= 0.401 Chirality : 0.053 0.465 490 Planarity : 0.005 0.045 595 Dihedral : 6.650 27.999 486 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.63 % Favored : 85.13 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.38), residues: 417 helix: -4.70 (0.63), residues: 19 sheet: -2.32 (0.39), residues: 164 loop : -2.64 (0.37), residues: 234 =============================================================================== Job complete usr+sys time: 1765.17 seconds wall clock time: 32 minutes 37.99 seconds (1957.99 seconds total)