Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:03:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1a_10669/11_2022/6y1a_10669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1a_10669/11_2022/6y1a_10669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1a_10669/11_2022/6y1a_10669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1a_10669/11_2022/6y1a_10669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1a_10669/11_2022/6y1a_10669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y1a_10669/11_2022/6y1a_10669_updated.pdb" } resolution = 4.2 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= 1.000 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 None 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: 2960 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "B" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "D" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "E" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "F" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "H" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "I" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "J" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "K" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "L" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "M" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "N" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "O" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "P" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.82, per 1000 atoms: 0.61 Number of scatterers: 2960 At special positions: 0 Unit cell: (61.71, 66.385, 55.165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 608 8.00 N 528 7.00 C 1824 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 425.1 milliseconds 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 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: 0.22 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: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 480 1.29 - 1.36: 512 1.36 - 1.42: 416 1.42 - 1.48: 416 1.48 - 1.55: 1168 Bond restraints: 2992 Sorted by residual: bond pdb=" N ALA M 13 " pdb=" CA ALA M 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N ALA B 13 " pdb=" CA ALA B 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N ALA E 13 " pdb=" CA ALA E 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ALA N 13 " pdb=" CA ALA N 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N ALA J 13 " pdb=" CA ALA J 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 ... (remaining 2987 not shown) Histogram of bond angle deviations from ideal: 106.02 - 111.07: 1294 111.07 - 116.11: 668 116.11 - 121.15: 1225 121.15 - 126.20: 861 126.20 - 131.24: 16 Bond angle restraints: 4064 Sorted by residual: angle pdb=" N THR D 36 " pdb=" CA THR D 36 " pdb=" C THR D 36 " ideal model delta sigma weight residual 109.24 113.99 -4.75 1.67e+00 3.59e-01 8.10e+00 angle pdb=" N THR C 36 " pdb=" CA THR C 36 " pdb=" C THR C 36 " ideal model delta sigma weight residual 109.24 113.97 -4.73 1.67e+00 3.59e-01 8.02e+00 angle pdb=" N THR E 36 " pdb=" CA THR E 36 " pdb=" C THR E 36 " ideal model delta sigma weight residual 109.24 113.96 -4.72 1.67e+00 3.59e-01 8.00e+00 angle pdb=" N THR L 36 " pdb=" CA THR L 36 " pdb=" C THR L 36 " ideal model delta sigma weight residual 109.24 113.95 -4.71 1.67e+00 3.59e-01 7.95e+00 angle pdb=" N THR I 36 " pdb=" CA THR I 36 " pdb=" C THR I 36 " ideal model delta sigma weight residual 109.24 113.92 -4.68 1.67e+00 3.59e-01 7.87e+00 ... (remaining 4059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.00: 1472 6.00 - 12.00: 50 12.00 - 18.00: 46 18.00 - 23.99: 26 23.99 - 29.99: 70 Dihedral angle restraints: 1664 sinusoidal: 528 harmonic: 1136 Sorted by residual: dihedral pdb=" CA ASN L 31 " pdb=" CB ASN L 31 " pdb=" CG ASN L 31 " pdb=" OD1 ASN L 31 " ideal model delta sinusoidal sigma weight residual -30.00 -59.99 29.99 2 2.00e+01 2.50e-03 3.00e+00 dihedral pdb=" CA ASN O 31 " pdb=" CB ASN O 31 " pdb=" CG ASN O 31 " pdb=" OD1 ASN O 31 " ideal model delta sinusoidal sigma weight residual -90.00 -60.02 -29.98 2 2.00e+01 2.50e-03 3.00e+00 dihedral pdb=" CA ASN I 31 " pdb=" CB ASN I 31 " pdb=" CG ASN I 31 " pdb=" OD1 ASN I 31 " ideal model delta sinusoidal sigma weight residual -30.00 -59.98 29.98 2 2.00e+01 2.50e-03 3.00e+00 ... (remaining 1661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 171 0.035 - 0.069: 167 0.069 - 0.103: 87 0.103 - 0.138: 39 0.138 - 0.172: 16 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA VAL G 32 " pdb=" N VAL G 32 " pdb=" C VAL G 32 " pdb=" CB VAL G 32 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA VAL A 32 " pdb=" N VAL A 32 " pdb=" C VAL A 32 " pdb=" CB VAL A 32 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA VAL E 32 " pdb=" N VAL E 32 " pdb=" C VAL E 32 " pdb=" CB VAL E 32 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 477 not shown) Planarity restraints: 528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR K 36 " 0.002 2.00e-02 2.50e+03 4.08e-03 1.67e-01 pdb=" C THR K 36 " -0.007 2.00e-02 2.50e+03 pdb=" O THR K 36 " 0.003 2.00e-02 2.50e+03 pdb=" N TYR K 37 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 36 " -0.002 2.00e-02 2.50e+03 4.08e-03 1.66e-01 pdb=" C THR P 36 " 0.007 2.00e-02 2.50e+03 pdb=" O THR P 36 " -0.003 2.00e-02 2.50e+03 pdb=" N TYR P 37 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 36 " -0.002 2.00e-02 2.50e+03 3.92e-03 1.53e-01 pdb=" C THR H 36 " 0.007 2.00e-02 2.50e+03 pdb=" O THR H 36 " -0.003 2.00e-02 2.50e+03 pdb=" N TYR H 37 " -0.002 2.00e-02 2.50e+03 ... (remaining 525 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1676 2.99 - 3.47: 2776 3.47 - 3.94: 5115 3.94 - 4.42: 5472 4.42 - 4.90: 10579 Nonbonded interactions: 25618 Sorted by model distance: nonbonded pdb=" OG SER G 19 " pdb=" OD1 ASN G 22 " model vdw 2.509 2.440 nonbonded pdb=" OG SER D 19 " pdb=" OD1 ASN D 22 " model vdw 2.510 2.440 nonbonded pdb=" OG SER H 19 " pdb=" OD1 ASN H 22 " model vdw 2.510 2.440 nonbonded pdb=" OG SER K 19 " pdb=" OD1 ASN K 22 " model vdw 2.510 2.440 nonbonded pdb=" OG SER J 19 " pdb=" OD1 ASN J 22 " model vdw 2.510 2.440 ... (remaining 25613 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 3 Type Number sf(0) Gaussians C 1824 2.51 5 N 528 2.21 5 O 608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 1.820 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 11.860 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 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 0.033 2992 Z= 0.304 Angle : 1.094 4.752 4064 Z= 0.710 Chirality : 0.067 0.172 480 Planarity : 0.001 0.004 528 Dihedral : 9.418 29.993 928 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: -4.99 (0.21), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.16), residues: 368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.344 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0714 time to fit residues: 11.7431 Evaluate side-chains 44 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 0.0370 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN C 31 ASN ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN E 31 ASN F 31 ASN G 31 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN I 31 ASN K 31 ASN L 31 ASN M 31 ASN N 31 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 2992 Z= 0.255 Angle : 0.535 5.086 4064 Z= 0.296 Chirality : 0.039 0.126 480 Planarity : 0.002 0.011 528 Dihedral : 4.111 14.305 400 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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: -4.80 (0.26), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.20), residues: 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.346 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0713 time to fit residues: 5.7208 Evaluate side-chains 32 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 30.0000 chunk 25 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 14 ASN C 31 ASN ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN E 31 ASN F 35 ASN G 31 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN H 35 ASN I 31 ASN K 31 ASN L 35 ASN M 31 ASN ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.6460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 2992 Z= 0.325 Angle : 0.541 8.180 4064 Z= 0.293 Chirality : 0.038 0.137 480 Planarity : 0.003 0.010 528 Dihedral : 4.759 16.966 400 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % 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: -4.75 (0.29), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.22), residues: 368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.361 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0723 time to fit residues: 4.1086 Evaluate side-chains 23 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN I 31 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN M 31 ASN P 35 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 2992 Z= 0.214 Angle : 0.474 6.594 4064 Z= 0.242 Chirality : 0.037 0.125 480 Planarity : 0.002 0.008 528 Dihedral : 4.021 14.159 400 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: -4.86 (0.28), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.22), residues: 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0712 time to fit residues: 3.9599 Evaluate side-chains 28 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 overall best weight: 7.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS I 31 ASN M 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 2992 Z= 0.385 Angle : 0.561 6.843 4064 Z= 0.307 Chirality : 0.039 0.146 480 Planarity : 0.003 0.010 528 Dihedral : 5.135 20.018 400 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % 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: -5.04 (0.27), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.20), residues: 368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.347 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0735 time to fit residues: 2.9660 Evaluate side-chains 19 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 14 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN D 18 HIS ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.7838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 2992 Z= 0.332 Angle : 0.571 6.734 4064 Z= 0.297 Chirality : 0.038 0.124 480 Planarity : 0.002 0.013 528 Dihedral : 5.089 19.491 400 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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: -5.14 (0.26), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.20), residues: 368 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.356 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0721 time to fit residues: 2.9343 Evaluate side-chains 20 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 14 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.8256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 2992 Z= 0.341 Angle : 0.595 7.053 4064 Z= 0.308 Chirality : 0.038 0.121 480 Planarity : 0.003 0.016 528 Dihedral : 5.437 19.215 400 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % 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: -5.11 (0.25), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.19), residues: 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.332 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0701 time to fit residues: 2.8400 Evaluate side-chains 22 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 HIS L 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.8457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 2992 Z= 0.318 Angle : 0.569 6.871 4064 Z= 0.295 Chirality : 0.039 0.133 480 Planarity : 0.002 0.012 528 Dihedral : 5.322 18.824 400 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % 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: -4.98 (0.26), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.19), residues: 368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0689 time to fit residues: 2.8809 Evaluate side-chains 22 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.8365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 2992 Z= 0.194 Angle : 0.513 6.991 4064 Z= 0.254 Chirality : 0.038 0.150 480 Planarity : 0.002 0.015 528 Dihedral : 4.403 14.535 400 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.26), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.20), residues: 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.376 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.0716 time to fit residues: 3.5742 Evaluate side-chains 26 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.8720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 2992 Z= 0.373 Angle : 0.593 7.312 4064 Z= 0.316 Chirality : 0.039 0.132 480 Planarity : 0.003 0.012 528 Dihedral : 5.606 17.790 400 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.76 % Favored : 84.24 % 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: -4.89 (0.27), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.21), residues: 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.340 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0691 time to fit residues: 2.9223 Evaluate side-chains 23 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 0.0370 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 overall best weight: 6.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.078911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.068997 restraints weight = 10512.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.070601 restraints weight = 5293.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.071825 restraints weight = 3532.961| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.8769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 2992 Z= 0.327 Angle : 0.571 6.918 4064 Z= 0.302 Chirality : 0.039 0.145 480 Planarity : 0.002 0.011 528 Dihedral : 5.469 17.362 400 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % 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: -4.83 (0.27), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.20), residues: 368 =============================================================================== Job complete usr+sys time: 818.21 seconds wall clock time: 16 minutes 6.89 seconds (966.89 seconds total)