Mon 24 Dec 00:44:19 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2prr-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.2-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.2-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:44:23 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-3.2-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1940 and 0 Target number of residues in the AU: 1940 Target solvent content: 0.6319 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 2364 Adjusted target solvent content: 0.55 Input MTZ file: 2prr-3.2-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 119.307 3.200 Wilson plot Bfac: 67.47 44474 reflections ( 97.55 % complete ) and 0 restraints for refining 20862 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.2910 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2106 (Rfree = 0.000) for 20862 atoms. Found 103 (187 requested) and removed 145 (93 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.01 Search for helices and strands: 0 residues in 0 chains, 21430 seeds are put forward NCS extension: 0 residues added, 21430 seeds are put forward Round 1: 1417 peptides, 239 chains. Longest chain 22 peptides. Score 0.444 Round 2: 1563 peptides, 207 chains. Longest chain 22 peptides. Score 0.581 Round 3: 1583 peptides, 194 chains. Longest chain 23 peptides. Score 0.614 Round 4: 1628 peptides, 183 chains. Longest chain 31 peptides. Score 0.651 Round 5: 1618 peptides, 183 chains. Longest chain 28 peptides. Score 0.647 Taking the results from Round 4 Chains 194, Residues 1445, Estimated correctness of the model 54.1 % 23 chains (320 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 6791 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2101 (Rfree = 0.000) for 17266 atoms. Found 94 (154 requested) and removed 116 (77 requested) atoms. Cycle 2: After refmac, R = 0.1930 (Rfree = 0.000) for 17244 atoms. Found 66 (154 requested) and removed 87 (77 requested) atoms. Cycle 3: After refmac, R = 0.1862 (Rfree = 0.000) for 17223 atoms. Found 23 (154 requested) and removed 89 (77 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1809 (Rfree = 0.000) for 17157 atoms. Found 22 (153 requested) and removed 83 (76 requested) atoms. Cycle 5: After refmac, R = 0.1776 (Rfree = 0.000) for 17096 atoms. Found 20 (153 requested) and removed 80 (76 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 17742 seeds are put forward NCS extension: 6 residues added (12 deleted due to clashes), 17748 seeds are put forward Round 1: 1532 peptides, 212 chains. Longest chain 23 peptides. Score 0.557 Round 2: 1637 peptides, 185 chains. Longest chain 40 peptides. Score 0.651 Round 3: 1680 peptides, 187 chains. Longest chain 35 peptides. Score 0.663 Round 4: 1629 peptides, 176 chains. Longest chain 33 peptides. Score 0.663 Round 5: 1644 peptides, 186 chains. Longest chain 37 peptides. Score 0.652 Taking the results from Round 4 Chains 184, Residues 1453, Estimated correctness of the model 56.9 % 20 chains (292 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 44474 reflections ( 97.55 % complete ) and 6753 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2046 (Rfree = 0.000) for 17266 atoms. Found 86 (154 requested) and removed 115 (77 requested) atoms. Cycle 7: After refmac, R = 0.1907 (Rfree = 0.000) for 17237 atoms. Found 30 (154 requested) and removed 83 (77 requested) atoms. Cycle 8: After refmac, R = 0.1859 (Rfree = 0.000) for 17184 atoms. Found 29 (154 requested) and removed 78 (77 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1834 (Rfree = 0.000) for 17135 atoms. Found 19 (153 requested) and removed 81 (76 requested) atoms. Cycle 10: After refmac, R = 0.1808 (Rfree = 0.000) for 17073 atoms. Found 27 (153 requested) and removed 77 (76 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17740 seeds are put forward NCS extension: 16 residues added (18 deleted due to clashes), 17756 seeds are put forward Round 1: 1486 peptides, 211 chains. Longest chain 24 peptides. Score 0.538 Round 2: 1564 peptides, 184 chains. Longest chain 37 peptides. Score 0.624 Round 3: 1612 peptides, 195 chains. Longest chain 22 peptides. Score 0.623 Round 4: 1607 peptides, 193 chains. Longest chain 37 peptides. Score 0.625 Round 5: 1585 peptides, 188 chains. Longest chain 37 peptides. Score 0.625 Taking the results from Round 5 Chains 196, Residues 1397, Estimated correctness of the model 47.6 % 20 chains (287 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 6529 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2092 (Rfree = 0.000) for 17266 atoms. Found 77 (154 requested) and removed 126 (77 requested) atoms. Cycle 12: After refmac, R = 0.1975 (Rfree = 0.000) for 17217 atoms. Found 52 (154 requested) and removed 90 (77 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1922 (Rfree = 0.000) for 17179 atoms. Found 30 (154 requested) and removed 81 (77 requested) atoms. Cycle 14: After refmac, R = 0.1883 (Rfree = 0.000) for 17128 atoms. Found 39 (153 requested) and removed 80 (76 requested) atoms. Cycle 15: After refmac, R = 0.1839 (Rfree = 0.000) for 17087 atoms. Found 22 (153 requested) and removed 78 (76 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 17711 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 17730 seeds are put forward Round 1: 1401 peptides, 219 chains. Longest chain 18 peptides. Score 0.480 Round 2: 1561 peptides, 204 chains. Longest chain 27 peptides. Score 0.586 Round 3: 1504 peptides, 199 chains. Longest chain 22 peptides. Score 0.571 Round 4: 1513 peptides, 192 chains. Longest chain 40 peptides. Score 0.588 Round 5: 1525 peptides, 194 chains. Longest chain 22 peptides. Score 0.589 Taking the results from Round 5 Chains 202, Residues 1331, Estimated correctness of the model 38.1 % 15 chains (151 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5750 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2030 (Rfree = 0.000) for 17266 atoms. Found 74 (154 requested) and removed 99 (77 requested) atoms. Cycle 17: After refmac, R = 0.1900 (Rfree = 0.000) for 17241 atoms. Found 39 (154 requested) and removed 82 (77 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1896 (Rfree = 0.000) for 17198 atoms. Found 48 (154 requested) and removed 78 (77 requested) atoms. Cycle 19: After refmac, R = 0.1828 (Rfree = 0.000) for 17168 atoms. Found 34 (154 requested) and removed 79 (77 requested) atoms. Cycle 20: After refmac, R = 0.1823 (Rfree = 0.000) for 17123 atoms. Found 33 (153 requested) and removed 81 (76 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17804 seeds are put forward NCS extension: 10 residues added (8 deleted due to clashes), 17814 seeds are put forward Round 1: 1288 peptides, 198 chains. Longest chain 23 peptides. Score 0.469 Round 2: 1455 peptides, 183 chains. Longest chain 20 peptides. Score 0.581 Round 3: 1452 peptides, 182 chains. Longest chain 28 peptides. Score 0.581 Round 4: 1440 peptides, 190 chains. Longest chain 22 peptides. Score 0.560 Round 5: 1448 peptides, 182 chains. Longest chain 28 peptides. Score 0.580 Taking the results from Round 3 Chains 187, Residues 1270, Estimated correctness of the model 35.8 % 13 chains (133 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5395 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1927 (Rfree = 0.000) for 17266 atoms. Found 88 (154 requested) and removed 94 (77 requested) atoms. Cycle 22: After refmac, R = 0.1832 (Rfree = 0.000) for 17260 atoms. Found 51 (154 requested) and removed 81 (77 requested) atoms. Cycle 23: After refmac, R = 0.1770 (Rfree = 0.000) for 17230 atoms. Found 38 (154 requested) and removed 82 (77 requested) atoms. Cycle 24: After refmac, R = 0.1761 (Rfree = 0.000) for 17186 atoms. Found 37 (154 requested) and removed 80 (77 requested) atoms. Cycle 25: After refmac, R = 0.1720 (Rfree = 0.000) for 17143 atoms. Found 29 (153 requested) and removed 78 (76 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 3.04 Search for helices and strands: 0 residues in 0 chains, 17786 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 17798 seeds are put forward Round 1: 1291 peptides, 202 chains. Longest chain 26 peptides. Score 0.462 Round 2: 1456 peptides, 195 chains. Longest chain 28 peptides. Score 0.557 Round 3: 1470 peptides, 200 chains. Longest chain 22 peptides. Score 0.553 Round 4: 1470 peptides, 193 chains. Longest chain 23 peptides. Score 0.567 Round 5: 1446 peptides, 195 chains. Longest chain 27 peptides. Score 0.553 Taking the results from Round 4 Chains 199, Residues 1277, Estimated correctness of the model 31.9 % 9 chains (100 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5283 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1935 (Rfree = 0.000) for 17266 atoms. Found 96 (154 requested) and removed 110 (77 requested) atoms. Cycle 27: After refmac, R = 0.1803 (Rfree = 0.000) for 17252 atoms. Found 32 (154 requested) and removed 81 (77 requested) atoms. Cycle 28: After refmac, R = 0.1787 (Rfree = 0.000) for 17203 atoms. Found 43 (154 requested) and removed 80 (77 requested) atoms. Cycle 29: After refmac, R = 0.1753 (Rfree = 0.000) for 17166 atoms. Found 35 (154 requested) and removed 79 (77 requested) atoms. Cycle 30: After refmac, R = 0.1740 (Rfree = 0.000) for 17122 atoms. Found 30 (153 requested) and removed 76 (76 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17786 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 17800 seeds are put forward Round 1: 1262 peptides, 202 chains. Longest chain 25 peptides. Score 0.446 Round 2: 1415 peptides, 184 chains. Longest chain 27 peptides. Score 0.561 Round 3: 1385 peptides, 174 chains. Longest chain 31 peptides. Score 0.568 Round 4: 1371 peptides, 174 chains. Longest chain 24 peptides. Score 0.561 Round 5: 1345 peptides, 173 chains. Longest chain 30 peptides. Score 0.552 Taking the results from Round 3 Chains 181, Residues 1211, Estimated correctness of the model 32.1 % 10 chains (107 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 5106 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1882 (Rfree = 0.000) for 17266 atoms. Found 64 (154 requested) and removed 93 (77 requested) atoms. Cycle 32: After refmac, R = 0.1815 (Rfree = 0.000) for 17237 atoms. Found 32 (154 requested) and removed 80 (77 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1792 (Rfree = 0.000) for 17189 atoms. Found 35 (154 requested) and removed 80 (77 requested) atoms. Cycle 34: After refmac, R = 0.1767 (Rfree = 0.000) for 17144 atoms. Found 26 (153 requested) and removed 78 (76 requested) atoms. Cycle 35: After refmac, R = 0.1745 (Rfree = 0.000) for 17092 atoms. Found 31 (153 requested) and removed 77 (76 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17697 seeds are put forward NCS extension: 36 residues added (3 deleted due to clashes), 17733 seeds are put forward Round 1: 1244 peptides, 198 chains. Longest chain 24 peptides. Score 0.446 Round 2: 1382 peptides, 191 chains. Longest chain 21 peptides. Score 0.531 Round 3: 1362 peptides, 185 chains. Longest chain 28 peptides. Score 0.534 Round 4: 1315 peptides, 182 chains. Longest chain 21 peptides. Score 0.518 Round 5: 1342 peptides, 185 chains. Longest chain 32 peptides. Score 0.525 Taking the results from Round 3 Chains 188, Residues 1177, Estimated correctness of the model 22.1 % 11 chains (99 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 4861 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1885 (Rfree = 0.000) for 17266 atoms. Found 66 (154 requested) and removed 98 (77 requested) atoms. Cycle 37: After refmac, R = 0.1809 (Rfree = 0.000) for 17234 atoms. Found 38 (154 requested) and removed 79 (77 requested) atoms. Cycle 38: After refmac, R = 0.1805 (Rfree = 0.000) for 17193 atoms. Found 41 (154 requested) and removed 79 (77 requested) atoms. Cycle 39: After refmac, R = 0.1798 (Rfree = 0.000) for 17155 atoms. Found 43 (153 requested) and removed 77 (76 requested) atoms. Cycle 40: After refmac, R = 0.1757 (Rfree = 0.000) for 17121 atoms. Found 39 (153 requested) and removed 80 (76 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17730 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 17746 seeds are put forward Round 1: 1126 peptides, 187 chains. Longest chain 25 peptides. Score 0.408 Round 2: 1244 peptides, 177 chains. Longest chain 27 peptides. Score 0.494 Round 3: 1272 peptides, 181 chains. Longest chain 20 peptides. Score 0.499 Round 4: 1266 peptides, 173 chains. Longest chain 30 peptides. Score 0.514 Round 5: 1257 peptides, 171 chains. Longest chain 29 peptides. Score 0.514 Taking the results from Round 5 Chains 176, Residues 1086, Estimated correctness of the model 15.8 % 8 chains (96 residues) have been docked in sequence ------------------------------------------------------ 44474 reflections ( 97.55 % complete ) and 4543 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1911 (Rfree = 0.000) for 17266 atoms. Found 75 (154 requested) and removed 93 (77 requested) atoms. Cycle 42: After refmac, R = 0.1816 (Rfree = 0.000) for 17248 atoms. Found 31 (154 requested) and removed 79 (77 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1790 (Rfree = 0.000) for 17200 atoms. Found 30 (154 requested) and removed 78 (77 requested) atoms. Cycle 44: After refmac, R = 0.1759 (Rfree = 0.000) for 17152 atoms. Found 38 (153 requested) and removed 80 (76 requested) atoms. Cycle 45: After refmac, R = 0.1737 (Rfree = 0.000) for 17110 atoms. Found 23 (153 requested) and removed 78 (76 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 17766 seeds are put forward NCS extension: 38 residues added (9 deleted due to clashes), 17804 seeds are put forward Round 1: 1074 peptides, 192 chains. Longest chain 25 peptides. Score 0.365 Round 2: 1230 peptides, 183 chains. Longest chain 24 peptides. Score 0.473 Round 3: 1240 peptides, 176 chains. Longest chain 20 peptides. Score 0.494 Round 4: 1230 peptides, 176 chains. Longest chain 24 peptides. Score 0.489 Round 5: 1239 peptides, 171 chains. Longest chain 27 peptides. Score 0.505 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 172, Residues 1068, Estimated correctness of the model 12.9 % 10 chains (63 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2prr-3_warpNtrace.pdb as input Building loops using Loopy2018 172 chains (1068 residues) following loop building 10 chains (63 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 44474 reflections ( 97.55 % complete ) and 4331 restraints for refining 17266 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1828 (Rfree = 0.000) for 17266 atoms. Found 0 (154 requested) and removed 30 (77 requested) atoms. Cycle 47: After refmac, R = 0.1780 (Rfree = 0.000) for 17236 atoms. Found 0 (154 requested) and removed 16 (77 requested) atoms. Cycle 48: After refmac, R = 0.1759 (Rfree = 0.000) for 17220 atoms. Found 0 (154 requested) and removed 18 (77 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1766 (Rfree = 0.000) for 17202 atoms. Found 0 (154 requested) and removed 23 (77 requested) atoms. Writing output files ... TimeTaking 164.3