Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:37:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/11_2022/7wp5_32669.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/11_2022/7wp5_32669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/11_2022/7wp5_32669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/11_2022/7wp5_32669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/11_2022/7wp5_32669.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/11_2022/7wp5_32669.pdb" } resolution = 3.9 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= 0.008 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 "F GLU 340": "OE1" <-> "OE2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" 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: 3340 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 811 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} 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: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1484 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 10, 'TRANS': 172} 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: 2.54, per 1000 atoms: 0.76 Number of scatterers: 3340 At special positions: 0 Unit cell: (77.022, 80.912, 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 644 8.00 N 563 7.00 C 2118 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=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 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: 1.21 Conformation dependent library (CDL) restraints added in 601.4 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 7 sheets defined 2.4% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.688A pdb=" N ASP F 339 " --> pdb=" O CYS F 336 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU F 340 " --> pdb=" O PRO F 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 336 through 340' Processing helix chain 'F' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.750A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 50 removed outlier: 5.740A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.600A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.790A 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: 3.618A pdb=" N GLY H 10 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR H 125 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 103 through 104 removed outlier: 3.606A pdb=" N TYR H 103 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN H 111 " --> pdb=" O TYR H 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 358 through 359 removed outlier: 3.735A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 376 through 379 removed outlier: 3.527A pdb=" N THR F 376 " --> pdb=" O ALA F 435 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 153 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: 0.77 Time building geometry restraints manager: 1.33 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: 1052 1.34 - 1.46: 852 1.46 - 1.58: 1503 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3426 Sorted by residual: bond pdb=" CA SER F 446 " pdb=" C SER F 446 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.37e-02 5.33e+03 2.59e+00 bond pdb=" CA CYS F 336 " pdb=" C CYS F 336 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.31e+00 bond pdb=" C4 NAG A 1 " pdb=" O4 NAG A 1 " ideal model delta sigma weight residual 1.423 1.435 -0.012 1.00e-02 1.00e+04 1.55e+00 bond pdb=" C CYS F 336 " pdb=" N PRO F 337 " ideal model delta sigma weight residual 1.337 1.349 -0.013 1.06e-02 8.90e+03 1.40e+00 bond pdb=" CG LEU F 425 " pdb=" CD1 LEU F 425 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 ... (remaining 3421 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.31: 89 106.31 - 113.22: 1712 113.22 - 120.14: 1241 120.14 - 127.05: 1560 127.05 - 133.97: 52 Bond angle restraints: 4654 Sorted by residual: angle pdb=" C ASN F 477 " pdb=" N LYS F 478 " pdb=" CA LYS F 478 " ideal model delta sigma weight residual 121.80 132.91 -11.11 2.44e+00 1.68e-01 2.07e+01 angle pdb=" C GLY L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C TYR F 369 " pdb=" N ASN F 370 " pdb=" CA ASN F 370 " ideal model delta sigma weight residual 122.19 128.42 -6.23 1.41e+00 5.03e-01 1.95e+01 angle pdb=" C SER F 359 " pdb=" N ASN F 360 " pdb=" CA ASN F 360 " ideal model delta sigma weight residual 122.46 128.68 -6.22 1.41e+00 5.03e-01 1.95e+01 angle pdb=" CA LEU F 371 " pdb=" CB LEU F 371 " pdb=" CG LEU F 371 " ideal model delta sigma weight residual 116.30 129.31 -13.01 3.50e+00 8.16e-02 1.38e+01 ... (remaining 4649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 1705 14.85 - 29.70: 218 29.70 - 44.55: 56 44.55 - 59.41: 6 59.41 - 74.26: 5 Dihedral angle restraints: 1990 sinusoidal: 770 harmonic: 1220 Sorted by residual: dihedral pdb=" CA ASN F 460 " pdb=" C ASN F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -147.27 -32.73 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA ASN F 477 " pdb=" C ASN F 477 " pdb=" N LYS F 478 " pdb=" CA LYS F 478 " ideal model delta harmonic sigma weight residual -180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ASN H 115 " pdb=" C ASN H 115 " pdb=" N TYR H 116 " pdb=" CA TYR H 116 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 1987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 395 0.066 - 0.132: 77 0.132 - 0.198: 21 0.198 - 0.264: 1 0.264 - 0.329: 1 Chirality restraints: 495 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 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 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 -2.37 -0.03 2.00e-02 2.50e+03 2.11e+00 chirality pdb=" CB THR H 91 " pdb=" CA THR H 91 " pdb=" OG1 THR H 91 " pdb=" CG2 THR H 91 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 492 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.278 2.00e-02 2.50e+03 2.38e-01 7.10e+02 pdb=" C7 NAG A 1 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.016 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.402 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.028 2.00e-02 2.50e+03 2.34e-02 6.84e+00 pdb=" C7 NAG A 2 " -0.007 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.021 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.037 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 411 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO F 412 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 412 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 412 " 0.029 5.00e-02 4.00e+02 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 935 2.80 - 3.33: 2725 3.33 - 3.85: 5189 3.85 - 4.38: 5630 4.38 - 4.90: 9998 Nonbonded interactions: 24477 Sorted by model distance: nonbonded pdb=" OD2 ASP F 442 " pdb=" OH TYR F 451 " model vdw 2.278 2.440 nonbonded pdb=" OD2 ASP F 398 " pdb=" OH TYR F 423 " model vdw 2.305 2.440 nonbonded pdb=" NE2 HIS L 36 " pdb=" O ASN H 115 " model vdw 2.326 2.520 nonbonded pdb=" NE2 GLN L 39 " pdb=" OD1 ASP L 84 " model vdw 2.364 2.520 nonbonded pdb=" OG SER H 130 " pdb=" N SER H 131 " model vdw 2.373 2.520 ... (remaining 24472 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 2118 2.51 5 N 563 2.21 5 O 644 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: 9.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 37.640 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.060 Process input model: 19.180 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 : 0.005 0.039 3426 Z= 0.322 Angle : 1.022 13.015 4654 Z= 0.566 Chirality : 0.060 0.329 495 Planarity : 0.012 0.238 603 Dihedral : 14.063 74.258 1215 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.07 % Favored : 90.69 % Rotamer Outliers : 0.56 % 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: -4.27 (0.34), residues: 419 helix: -5.34 (0.29), residues: 11 sheet: -1.85 (0.43), residues: 135 loop : -3.47 (0.29), residues: 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 113 average time/residue: 0.1730 time to fit residues: 23.2276 Evaluate side-chains 82 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0471 time to fit residues: 0.6176 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 11 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 81 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 ASN ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3426 Z= 0.202 Angle : 0.706 8.158 4654 Z= 0.358 Chirality : 0.047 0.237 495 Planarity : 0.004 0.031 603 Dihedral : 6.458 27.730 490 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.26 % Favored : 89.50 % Rotamer Outliers : 4.20 % 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: -3.72 (0.36), residues: 419 helix: -4.04 (1.06), residues: 13 sheet: -1.51 (0.42), residues: 143 loop : -3.12 (0.32), residues: 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.390 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 91 average time/residue: 0.1335 time to fit residues: 15.1183 Evaluate side-chains 91 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0366 time to fit residues: 1.1353 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 3426 Z= 0.169 Angle : 0.644 7.738 4654 Z= 0.325 Chirality : 0.045 0.181 495 Planarity : 0.004 0.028 603 Dihedral : 6.085 26.693 490 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.35 % Favored : 91.41 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.37), residues: 419 helix: -4.15 (0.94), residues: 13 sheet: -1.24 (0.44), residues: 136 loop : -3.01 (0.33), residues: 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.395 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1337 time to fit residues: 15.3867 Evaluate side-chains 88 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0330 time to fit residues: 0.9017 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.0030 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3426 Z= 0.227 Angle : 0.670 7.863 4654 Z= 0.339 Chirality : 0.046 0.193 495 Planarity : 0.004 0.028 603 Dihedral : 6.040 26.138 490 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.50 % Favored : 89.26 % Rotamer Outliers : 3.36 % 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: -3.42 (0.37), residues: 419 helix: -5.85 (0.26), residues: 5 sheet: -1.15 (0.42), residues: 143 loop : -3.03 (0.33), residues: 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.388 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 87 average time/residue: 0.1197 time to fit residues: 13.3871 Evaluate side-chains 83 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0373 time to fit residues: 0.9112 ------------------------------------------------------------------------------- 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: 0.4980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 3426 Z= 0.235 Angle : 0.662 8.033 4654 Z= 0.335 Chirality : 0.045 0.183 495 Planarity : 0.004 0.027 603 Dihedral : 6.019 26.713 490 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.50 % Favored : 89.26 % Rotamer Outliers : 2.52 % 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: -3.35 (0.37), residues: 419 helix: -5.84 (0.26), residues: 5 sheet: -1.14 (0.42), residues: 144 loop : -2.97 (0.33), residues: 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.395 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.1243 time to fit residues: 13.0134 Evaluate side-chains 83 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0338 time to fit residues: 0.8909 ------------------------------------------------------------------------------- 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: 1.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 3426 Z= 0.332 Angle : 0.755 8.727 4654 Z= 0.378 Chirality : 0.047 0.198 495 Planarity : 0.005 0.031 603 Dihedral : 6.384 31.529 490 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.93 % Favored : 87.83 % Rotamer Outliers : 5.04 % 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: -3.39 (0.37), residues: 419 helix: -5.84 (0.26), residues: 5 sheet: -1.15 (0.41), residues: 146 loop : -3.00 (0.33), residues: 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.388 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 90 average time/residue: 0.1171 time to fit residues: 13.5146 Evaluate side-chains 87 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0344 time to fit residues: 1.2453 ------------------------------------------------------------------------------- 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: 0.2980 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 25 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 3426 Z= 0.197 Angle : 0.714 8.843 4654 Z= 0.355 Chirality : 0.046 0.235 495 Planarity : 0.004 0.031 603 Dihedral : 6.109 25.527 490 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.83 % Favored : 90.93 % Rotamer Outliers : 0.84 % 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: -3.25 (0.37), residues: 419 helix: -5.82 (0.26), residues: 5 sheet: -1.13 (0.42), residues: 145 loop : -2.85 (0.34), residues: 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.327 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 75 average time/residue: 0.1157 time to fit residues: 11.3357 Evaluate side-chains 75 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0449 time to fit residues: 0.7311 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.0050 chunk 38 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3426 Z= 0.202 Angle : 0.679 7.999 4654 Z= 0.344 Chirality : 0.045 0.158 495 Planarity : 0.004 0.031 603 Dihedral : 5.986 25.466 490 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.50 % Favored : 89.26 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.38), residues: 419 helix: -5.81 (0.25), residues: 5 sheet: -1.01 (0.43), residues: 138 loop : -2.63 (0.34), residues: 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.416 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 0.1163 time to fit residues: 11.2789 Evaluate side-chains 76 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0364 time to fit residues: 0.8512 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 : 0.004 0.035 3426 Z= 0.246 Angle : 0.700 8.154 4654 Z= 0.355 Chirality : 0.045 0.149 495 Planarity : 0.004 0.032 603 Dihedral : 6.139 27.537 490 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.98 % Favored : 88.78 % Rotamer Outliers : 0.56 % 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: -3.06 (0.38), residues: 419 helix: -5.81 (0.24), residues: 5 sheet: -1.06 (0.42), residues: 147 loop : -2.69 (0.35), residues: 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.393 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 0.1110 time to fit residues: 11.4040 Evaluate side-chains 71 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5019 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 3426 Z= 0.291 Angle : 0.722 8.529 4654 Z= 0.370 Chirality : 0.046 0.153 495 Planarity : 0.004 0.032 603 Dihedral : 6.240 29.254 490 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.41 % Favored : 87.35 % Rotamer Outliers : 0.84 % 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: -3.07 (0.38), residues: 419 helix: -5.80 (0.24), residues: 5 sheet: -1.04 (0.42), residues: 147 loop : -2.71 (0.34), residues: 267 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.375 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 71 average time/residue: 0.1121 time to fit residues: 10.4511 Evaluate side-chains 74 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0390 time to fit residues: 0.6791 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.0070 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.0270 chunk 41 optimal weight: 0.9980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 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 = 0.3989 r_free = 0.3989 target = 0.168269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.152734 restraints weight = 6367.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.157139 restraints weight = 5003.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.158989 restraints weight = 2317.196| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3988 r_free = 0.3988 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 3426 Z= 0.190 Angle : 0.709 12.810 4654 Z= 0.353 Chirality : 0.046 0.228 495 Planarity : 0.004 0.031 603 Dihedral : 5.927 25.459 490 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.79 % Favored : 89.98 % 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: -2.83 (0.39), residues: 419 helix: -5.79 (0.24), residues: 5 sheet: -0.92 (0.44), residues: 139 loop : -2.47 (0.35), residues: 275 =============================================================================== Job complete usr+sys time: 1506.03 seconds wall clock time: 28 minutes 5.29 seconds (1685.29 seconds total)