Starting phenix.real_space_refine (version: dev) on Thu Feb 16 23:57:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2023/7wmm_32615_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2023/7wmm_32615.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2023/7wmm_32615_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2023/7wmm_32615_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2023/7wmm_32615_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2023/7wmm_32615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2023/7wmm_32615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2023/7wmm_32615_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2023/7wmm_32615_neut_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped None 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: 2618 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "B" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "C" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "D" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "E" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "F" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ASER A 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 42 " occ=0.50 residue: pdb=" N ASER B 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 42 " occ=0.50 residue: pdb=" N ASER C 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 42 " occ=0.50 residue: pdb=" N ASER D 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 42 " occ=0.50 residue: pdb=" N ASER E 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 42 " occ=0.50 residue: pdb=" N ASER F 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER F 42 " occ=0.50 Time building chain proxies: 3.09, per 1000 atoms: 1.18 Number of scatterers: 2618 At special positions: 0 Unit cell: (98.77, 105.41, 30.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 2 34.99 S 2 16.00 F 2 9.00 O 514 8.00 N 448 7.00 C 1650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 792.2 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 850 1.37 - 1.51: 864 1.51 - 1.66: 922 1.66 - 1.80: 2 1.80 - 1.94: 2 Bond restraints: 2640 Sorted by residual: bond pdb=" C16 1KI A 201 " pdb=" S27 1KI A 201 " ideal model delta sigma weight residual 1.538 1.669 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" C16 1KI C 201 " pdb=" S27 1KI C 201 " ideal model delta sigma weight residual 1.538 1.668 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C14 1KI C 201 " pdb=" N15 1KI C 201 " ideal model delta sigma weight residual 1.579 1.453 0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C14 1KI A 201 " pdb=" N15 1KI A 201 " ideal model delta sigma weight residual 1.579 1.454 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C13 1KI C 201 " pdb=" S27 1KI C 201 " ideal model delta sigma weight residual 1.533 1.656 -0.123 2.00e-02 2.50e+03 3.80e+01 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.14: 4 105.14 - 111.84: 1490 111.84 - 118.54: 715 118.54 - 125.23: 1361 125.23 - 131.93: 10 Bond angle restraints: 3580 Sorted by residual: angle pdb=" C01 1KI A 201 " pdb=" C02 1KI A 201 " pdb=" C28 1KI A 201 " ideal model delta sigma weight residual 98.51 119.44 -20.93 3.00e+00 1.11e-01 4.87e+01 angle pdb=" C01 1KI C 201 " pdb=" C02 1KI C 201 " pdb=" C28 1KI C 201 " ideal model delta sigma weight residual 98.51 119.40 -20.89 3.00e+00 1.11e-01 4.85e+01 angle pdb=" C01 1KI A 201 " pdb=" C02 1KI A 201 " pdb=" C03 1KI A 201 " ideal model delta sigma weight residual 140.71 120.24 20.47 3.00e+00 1.11e-01 4.65e+01 angle pdb=" C01 1KI C 201 " pdb=" C02 1KI C 201 " pdb=" C03 1KI C 201 " ideal model delta sigma weight residual 140.71 120.28 20.43 3.00e+00 1.11e-01 4.64e+01 angle pdb=" C17 1KI C 201 " pdb=" C18 1KI C 201 " pdb=" C19 1KI C 201 " ideal model delta sigma weight residual 120.00 103.75 16.25 3.00e+00 1.11e-01 2.93e+01 ... (remaining 3575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 1447 16.30 - 32.60: 47 32.60 - 48.90: 15 48.90 - 65.20: 7 65.20 - 81.50: 8 Dihedral angle restraints: 1524 sinusoidal: 510 harmonic: 1014 Sorted by residual: dihedral pdb=" CB GLU D 46 " pdb=" CG GLU D 46 " pdb=" CD GLU D 46 " pdb=" OE1 GLU D 46 " ideal model delta sinusoidal sigma weight residual 0.00 81.50 -81.50 1 3.00e+01 1.11e-03 9.09e+00 dihedral pdb=" CB GLU C 46 " pdb=" CG GLU C 46 " pdb=" CD GLU C 46 " pdb=" OE1 GLU C 46 " ideal model delta sinusoidal sigma weight residual 0.00 81.47 -81.47 1 3.00e+01 1.11e-03 9.09e+00 dihedral pdb=" CB GLU F 46 " pdb=" CG GLU F 46 " pdb=" CD GLU F 46 " pdb=" OE1 GLU F 46 " ideal model delta sinusoidal sigma weight residual 0.00 81.40 -81.40 1 3.00e+01 1.11e-03 9.07e+00 ... (remaining 1521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 158 0.025 - 0.049: 182 0.049 - 0.074: 41 0.074 - 0.099: 18 0.099 - 0.123: 63 Chirality restraints: 462 Sorted by residual: chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 459 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.005 2.00e-02 2.50e+03 5.43e-03 4.42e-01 pdb=" CG HIS A 50 " -0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " 0.005 2.00e-02 2.50e+03 5.32e-03 4.25e-01 pdb=" CG HIS B 50 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " 0.005 2.00e-02 2.50e+03 5.15e-03 3.98e-01 pdb=" CG HIS E 50 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " 0.002 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 812 2.87 - 3.38: 2181 3.38 - 3.88: 4359 3.88 - 4.39: 4421 4.39 - 4.90: 9021 Nonbonded interactions: 20794 Sorted by model distance: nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS E 80 " model vdw 2.361 2.520 nonbonded pdb=" NZ LYS A 80 " pdb=" OE1 GLU B 46 " model vdw 2.366 2.520 nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS F 80 " model vdw 2.377 2.520 nonbonded pdb=" NZ LYS C 80 " pdb=" OE1 GLU D 46 " model vdw 2.378 2.520 nonbonded pdb=" OE1 GLU A 83 " pdb=" F10 1KI A 201 " model vdw 2.458 2.390 ... (remaining 20789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'B' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'C' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'D' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'E' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'F' and (resid 37 through 41 or resid 43 through 97)) } 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: 6 Type Number sf(0) Gaussians Br 2 7.06 5 S 2 5.16 5 C 1650 2.51 5 N 448 2.21 5 O 514 1.98 5 F 2 1.80 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 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: 9.380 Check model and map are aligned: 0.030 Process input model: 12.550 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.131 2640 Z= 0.378 Angle : 1.097 20.933 3580 Z= 0.435 Chirality : 0.053 0.123 462 Planarity : 0.002 0.005 440 Dihedral : 12.991 81.499 888 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.39), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.30), residues: 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 1.4554 time to fit residues: 106.7265 Evaluate side-chains 58 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.266 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 2640 Z= 0.104 Angle : 0.608 8.379 3580 Z= 0.284 Chirality : 0.053 0.127 462 Planarity : 0.003 0.019 440 Dihedral : 7.418 72.390 390 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.38 % 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: -2.41 (0.41), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.31), residues: 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.298 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 1.0403 time to fit residues: 68.3172 Evaluate side-chains 60 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 0.2980 chunk 22 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.020 2640 Z= 0.198 Angle : 0.702 10.428 3580 Z= 0.342 Chirality : 0.056 0.131 462 Planarity : 0.002 0.014 440 Dihedral : 7.715 69.066 390 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % 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: -2.43 (0.41), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.32), residues: 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.301 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 58 average time/residue: 1.1115 time to fit residues: 66.1227 Evaluate side-chains 57 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0687 time to fit residues: 0.4096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 2640 Z= 0.089 Angle : 0.565 8.420 3580 Z= 0.264 Chirality : 0.052 0.124 462 Planarity : 0.002 0.013 440 Dihedral : 7.312 68.175 390 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.76 % 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: -2.16 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.33), residues: 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.322 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 1.0497 time to fit residues: 61.4739 Evaluate side-chains 55 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.0040 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 overall best weight: 3.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.023 2640 Z= 0.227 Angle : 0.710 10.380 3580 Z= 0.349 Chirality : 0.057 0.136 462 Planarity : 0.002 0.012 440 Dihedral : 7.578 70.162 390 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer Outliers : 0.76 % 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: -2.31 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.32), residues: 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.297 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 1.2099 time to fit residues: 70.6674 Evaluate side-chains 57 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0777 time to fit residues: 0.4794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 chunk 16 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 2640 Z= 0.071 Angle : 0.531 7.919 3580 Z= 0.244 Chirality : 0.051 0.121 462 Planarity : 0.002 0.012 440 Dihedral : 6.874 67.119 390 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.44), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.34), residues: 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.296 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 1.0503 time to fit residues: 60.3524 Evaluate side-chains 54 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.252 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.021 2640 Z= 0.207 Angle : 0.685 9.741 3580 Z= 0.335 Chirality : 0.056 0.133 462 Planarity : 0.002 0.010 440 Dihedral : 7.332 69.110 390 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 0.38 % 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: -2.15 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.33), residues: 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.346 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 1.3440 time to fit residues: 82.5887 Evaluate side-chains 59 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 0.0040 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 2640 Z= 0.081 Angle : 0.553 7.778 3580 Z= 0.257 Chirality : 0.052 0.123 462 Planarity : 0.002 0.012 440 Dihedral : 6.974 66.408 390 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.44), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.34), residues: 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.307 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 1.0823 time to fit residues: 60.0524 Evaluate side-chains 54 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 2640 Z= 0.128 Angle : 0.604 8.290 3580 Z= 0.289 Chirality : 0.053 0.127 462 Planarity : 0.002 0.011 440 Dihedral : 7.132 66.599 390 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.440 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 1.1637 time to fit residues: 72.6854 Evaluate side-chains 59 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.0370 chunk 30 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 0.0010 overall best weight: 1.5868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 2640 Z= 0.114 Angle : 0.596 8.081 3580 Z= 0.285 Chirality : 0.052 0.126 462 Planarity : 0.002 0.016 440 Dihedral : 6.786 64.707 390 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.44), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.33), residues: 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.277 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 1.1185 time to fit residues: 67.5999 Evaluate side-chains 59 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.252 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.151668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.116825 restraints weight = 13742.694| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.73 r_work: 0.3608 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4238 r_free = 0.4238 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4237 r_free = 0.4237 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 2640 Z= 0.135 Angle : 0.641 8.501 3580 Z= 0.307 Chirality : 0.053 0.128 462 Planarity : 0.002 0.017 440 Dihedral : 6.663 64.811 390 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.44), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.33), residues: 372 =============================================================================== Job complete usr+sys time: 1832.00 seconds wall clock time: 33 minutes 30.34 seconds (2010.34 seconds total)