Sun 23 Dec 22:23:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2isb-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2isb-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2isb-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.2-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:12 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/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.2-parrot-hancs/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 148 and 0 Target number of residues in the AU: 148 Target solvent content: 0.6196 Checking the provided sequence file Detected sequence length: 192 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 192 Adjusted target solvent content: 0.51 Input MTZ file: 2isb-3.2-parrot-hancs.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: 96 Cell parameters: 51.664 51.664 157.756 90.000 90.000 90.000 Input sequence file: 2isb-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1536 target number of atoms Had to go as low as 0.65 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. Conditional restraints will be used 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 Loops will be built when appropriate and at the last cycle Resolution range: 49.098 3.200 Wilson plot Bfac: 60.65 3901 reflections ( 99.41 % complete ) and 0 restraints for refining 1697 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3225 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2589 (Rfree = 0.000) for 1697 atoms. Found 11 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 3.06 Search for helices and strands: 0 residues in 0 chains, 1723 seeds are put forward Round 1: 120 peptides, 17 chains. Longest chain 12 peptides. Score 0.563 Round 2: 136 peptides, 15 chains. Longest chain 18 peptides. Score 0.693 Round 3: 144 peptides, 11 chains. Longest chain 28 peptides. Score 0.796 Round 4: 152 peptides, 8 chains. Longest chain 47 peptides. Score 0.859 Round 5: 148 peptides, 12 chains. Longest chain 31 peptides. Score 0.793 Taking the results from Round 4 Chains 9, Residues 144, Estimated correctness of the model 91.3 % 4 chains (114 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 72 A Built loop between residues 117 A and 121 A 7 chains (151 residues) following loop building 2 chains (121 residues) in sequence following loop building ------------------------------------------------------ 3901 reflections ( 99.41 % complete ) and 1935 restraints for refining 1492 atoms. 868 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2761 (Rfree = 0.000) for 1492 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 2: After refmac, R = 0.2423 (Rfree = 0.000) for 1437 atoms. Found 9 (13 requested) and removed 11 (6 requested) atoms. Cycle 3: After refmac, R = 0.2561 (Rfree = 0.000) for 1418 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2287 (Rfree = 0.000) for 1399 atoms. Found 4 (11 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.2142 (Rfree = 0.000) for 1396 atoms. Found 2 (11 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 1411 seeds are put forward Round 1: 140 peptides, 13 chains. Longest chain 24 peptides. Score 0.748 Round 2: 147 peptides, 11 chains. Longest chain 33 peptides. Score 0.805 Round 3: 151 peptides, 10 chains. Longest chain 35 peptides. Score 0.830 Round 4: 148 peptides, 9 chains. Longest chain 56 peptides. Score 0.836 Round 5: 145 peptides, 11 chains. Longest chain 22 peptides. Score 0.799 Taking the results from Round 4 Chains 9, Residues 139, Estimated correctness of the model 88.5 % 4 chains (108 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 140 A and 145 A 8 chains (143 residues) following loop building 3 chains (112 residues) in sequence following loop building ------------------------------------------------------ 3901 reflections ( 99.41 % complete ) and 1937 restraints for refining 1403 atoms. 930 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2521 (Rfree = 0.000) for 1403 atoms. Found 9 (11 requested) and removed 15 (6 requested) atoms. Cycle 7: After refmac, R = 0.2273 (Rfree = 0.000) for 1388 atoms. Found 8 (11 requested) and removed 8 (6 requested) atoms. Cycle 8: After refmac, R = 0.2483 (Rfree = 0.000) for 1382 atoms. Found 10 (10 requested) and removed 7 (6 requested) atoms. Cycle 9: After refmac, R = 0.2413 (Rfree = 0.000) for 1383 atoms. Found 10 (10 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.2376 (Rfree = 0.000) for 1379 atoms. Found 10 (10 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 1404 seeds are put forward Round 1: 152 peptides, 14 chains. Longest chain 23 peptides. Score 0.774 Round 2: 155 peptides, 7 chains. Longest chain 54 peptides. Score 0.877 Round 3: 152 peptides, 12 chains. Longest chain 26 peptides. Score 0.805 Round 4: 161 peptides, 8 chains. Longest chain 55 peptides. Score 0.877 Round 5: 152 peptides, 12 chains. Longest chain 30 peptides. Score 0.805 Taking the results from Round 4 Chains 8, Residues 153, Estimated correctness of the model 93.2 % 3 chains (103 residues) have been docked in sequence Building loops using Loopy2018 8 chains (153 residues) following loop building 3 chains (103 residues) in sequence following loop building ------------------------------------------------------ 3901 reflections ( 99.41 % complete ) and 1934 restraints for refining 1403 atoms. 922 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2499 (Rfree = 0.000) for 1403 atoms. Found 10 (10 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.2389 (Rfree = 0.000) for 1386 atoms. Found 9 (9 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.2242 (Rfree = 0.000) for 1380 atoms. Found 9 (9 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2227 (Rfree = 0.000) for 1372 atoms. Found 9 (9 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.2116 (Rfree = 0.000) for 1372 atoms. Found 9 (9 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 1418 seeds are put forward Round 1: 144 peptides, 10 chains. Longest chain 29 peptides. Score 0.811 Round 2: 152 peptides, 9 chains. Longest chain 29 peptides. Score 0.846 Round 3: 153 peptides, 9 chains. Longest chain 32 peptides. Score 0.849 Round 4: 155 peptides, 12 chains. Longest chain 26 peptides. Score 0.813 Round 5: 153 peptides, 11 chains. Longest chain 44 peptides. Score 0.822 Taking the results from Round 3 Chains 10, Residues 144, Estimated correctness of the model 90.1 % 3 chains (67 residues) have been docked in sequence Building loops using Loopy2018 10 chains (144 residues) following loop building 3 chains (67 residues) in sequence following loop building ------------------------------------------------------ 3901 reflections ( 99.41 % complete ) and 2321 restraints for refining 1402 atoms. 1484 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2618 (Rfree = 0.000) for 1402 atoms. Found 8 (8 requested) and removed 17 (6 requested) atoms. Cycle 17: After refmac, R = 0.2599 (Rfree = 0.000) for 1387 atoms. Found 8 (8 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.2553 (Rfree = 0.000) for 1379 atoms. Found 8 (8 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.2470 (Rfree = 0.000) for 1374 atoms. Found 8 (8 requested) and removed 12 (6 requested) atoms. Cycle 20: After refmac, R = 0.2012 (Rfree = 0.000) for 1367 atoms. Found 1 (7 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.11 Search for helices and strands: 0 residues in 0 chains, 1405 seeds are put forward Round 1: 148 peptides, 11 chains. Longest chain 31 peptides. Score 0.808 Round 2: 153 peptides, 9 chains. Longest chain 32 peptides. Score 0.849 Round 3: 149 peptides, 9 chains. Longest chain 37 peptides. Score 0.839 Round 4: 147 peptides, 12 chains. Longest chain 28 peptides. Score 0.789 Round 5: 151 peptides, 14 chains. Longest chain 20 peptides. Score 0.770 Taking the results from Round 2 Chains 11, Residues 144, Estimated correctness of the model 90.1 % 3 chains (67 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 99 A and 108 A 9 chains (151 residues) following loop building 2 chains (75 residues) in sequence following loop building ------------------------------------------------------ 3901 reflections ( 99.41 % complete ) and 2185 restraints for refining 1403 atoms. 1301 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2270 (Rfree = 0.000) for 1403 atoms. Found 6 (7 requested) and removed 11 (6 requested) atoms. Cycle 22: After refmac, R = 0.2394 (Rfree = 0.000) for 1392 atoms. Found 7 (7 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.2404 (Rfree = 0.000) for 1384 atoms. Found 6 (7 requested) and removed 10 (6 requested) atoms. Cycle 24: After refmac, R = 0.2170 (Rfree = 0.000) for 1378 atoms. Found 6 (6 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.1929 (Rfree = 0.000) for 1373 atoms. Found 5 (6 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.11 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward Round 1: 147 peptides, 11 chains. Longest chain 34 peptides. Score 0.805 Round 2: 154 peptides, 10 chains. Longest chain 51 peptides. Score 0.838 Round 3: 160 peptides, 11 chains. Longest chain 35 peptides. Score 0.840 Round 4: 157 peptides, 11 chains. Longest chain 39 peptides. Score 0.833 Round 5: 152 peptides, 10 chains. Longest chain 50 peptides. Score 0.833 Taking the results from Round 3 Chains 13, Residues 149, Estimated correctness of the model 89.0 % 2 chains (59 residues) have been docked in sequence Building loops using Loopy2018 13 chains (149 residues) following loop building 2 chains (59 residues) in sequence following loop building ------------------------------------------------------ 3901 reflections ( 99.41 % complete ) and 2378 restraints for refining 1403 atoms. 1575 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2502 (Rfree = 0.000) for 1403 atoms. Found 6 (6 requested) and removed 15 (6 requested) atoms. Cycle 27: After refmac, R = 0.2498 (Rfree = 0.000) for 1388 atoms. Found 6 (6 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.2468 (Rfree = 0.000) for 1376 atoms. Found 6 (6 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.1954 (Rfree = 0.000) for 1371 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1849 (Rfree = 0.000) for 1368 atoms. Found 4 (6 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward Round 1: 145 peptides, 13 chains. Longest chain 23 peptides. Score 0.766 Round 2: 154 peptides, 8 chains. Longest chain 61 peptides. Score 0.863 Round 3: 150 peptides, 14 chains. Longest chain 25 peptides. Score 0.767 Round 4: 157 peptides, 10 chains. Longest chain 30 peptides. Score 0.845 Round 5: 150 peptides, 13 chains. Longest chain 22 peptides. Score 0.783 Taking the results from Round 2 Chains 9, Residues 146, Estimated correctness of the model 91.7 % 4 chains (108 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 A and 57 A 7 chains (150 residues) following loop building 3 chains (113 residues) in sequence following loop building ------------------------------------------------------ 3901 reflections ( 99.41 % complete ) and 1756 restraints for refining 1403 atoms. 714 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2451 (Rfree = 0.000) for 1403 atoms. Found 6 (6 requested) and removed 22 (6 requested) atoms. Cycle 32: After refmac, R = 0.2366 (Rfree = 0.000) for 1381 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2304 (Rfree = 0.000) for 1376 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.1954 (Rfree = 0.000) for 1368 atoms. Found 6 (6 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.1865 (Rfree = 0.000) for 1363 atoms. Found 4 (6 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 1396 seeds are put forward Round 1: 152 peptides, 9 chains. Longest chain 33 peptides. Score 0.846 Round 2: 157 peptides, 9 chains. Longest chain 55 peptides. Score 0.858 Round 3: 148 peptides, 10 chains. Longest chain 28 peptides. Score 0.822 Round 4: 159 peptides, 11 chains. Longest chain 51 peptides. Score 0.837 Round 5: 155 peptides, 10 chains. Longest chain 55 peptides. Score 0.841 Taking the results from Round 2 Chains 9, Residues 148, Estimated correctness of the model 91.1 % 3 chains (90 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 A and 56 A Built loop between residues 109 A and 112 A 7 chains (154 residues) following loop building 1 chains (96 residues) in sequence following loop building ------------------------------------------------------ 3901 reflections ( 99.41 % complete ) and 1967 restraints for refining 1403 atoms. 979 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2329 (Rfree = 0.000) for 1403 atoms. Found 6 (6 requested) and removed 13 (6 requested) atoms. Cycle 37: After refmac, R = 0.2236 (Rfree = 0.000) for 1391 atoms. Found 6 (6 requested) and removed 9 (6 requested) atoms. Cycle 38: After refmac, R = 0.2111 (Rfree = 0.000) for 1383 atoms. Found 5 (6 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.2174 (Rfree = 0.000) for 1378 atoms. Found 6 (6 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1854 (Rfree = 0.000) for 1372 atoms. Found 2 (6 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 1403 seeds are put forward Round 1: 145 peptides, 11 chains. Longest chain 40 peptides. Score 0.799 Round 2: 154 peptides, 8 chains. Longest chain 35 peptides. Score 0.863 Round 3: 147 peptides, 10 chains. Longest chain 30 peptides. Score 0.820 Round 4: 149 peptides, 10 chains. Longest chain 28 peptides. Score 0.825 Round 5: 156 peptides, 12 chains. Longest chain 30 peptides. Score 0.816 Taking the results from Round 2 Chains 8, Residues 146, Estimated correctness of the model 91.7 % 4 chains (105 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 A and 56 A Built loop between residues 82 A and 89 A 6 chains (156 residues) following loop building 2 chains (115 residues) in sequence following loop building ------------------------------------------------------ 3901 reflections ( 99.41 % complete ) and 1776 restraints for refining 1403 atoms. 706 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2310 (Rfree = 0.000) for 1403 atoms. Found 6 (6 requested) and removed 18 (6 requested) atoms. Cycle 42: After refmac, R = 0.2237 (Rfree = 0.000) for 1386 atoms. Found 6 (6 requested) and removed 10 (6 requested) atoms. Cycle 43: After refmac, R = 0.2153 (Rfree = 0.000) for 1378 atoms. Found 3 (6 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.2099 (Rfree = 0.000) for 1372 atoms. Found 4 (6 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2106 (Rfree = 0.000) for 1364 atoms. Found 6 (6 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 1409 seeds are put forward Round 1: 141 peptides, 10 chains. Longest chain 35 peptides. Score 0.802 Round 2: 156 peptides, 8 chains. Longest chain 51 peptides. Score 0.867 Round 3: 153 peptides, 10 chains. Longest chain 31 peptides. Score 0.836 Round 4: 146 peptides, 12 chains. Longest chain 42 peptides. Score 0.786 Round 5: 150 peptides, 9 chains. Longest chain 38 peptides. Score 0.841 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 148, Estimated correctness of the model 92.1 % 3 chains (104 residues) have been docked in sequence Sequence coverage is 69 % Consider running further cycles of model building using 2isb-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 53 A and 56 A Built loop between residues 82 A and 88 A 6 chains (155 residues) following loop building 1 chains (111 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3901 reflections ( 99.41 % complete ) and 1864 restraints for refining 1402 atoms. 813 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2319 (Rfree = 0.000) for 1402 atoms. Found 0 (6 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2317 (Rfree = 0.000) for 1392 atoms. Found 0 (6 requested) and removed 3 (6 requested) atoms. Cycle 48: After refmac, R = 0.2198 (Rfree = 0.000) for 1387 atoms. Found 0 (6 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1942 (Rfree = 0.000) for 1376 atoms. TimeTaking 31.82