Tue 25 Dec 19:30:29 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 2a2m-1.9-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a2m-1.9-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a2m-1.9-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-1.9-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/2a2m-1.9-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-1.9-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 ============================================================ Tue 25 Dec 19:30:39 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/2a2m-1.9-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-1.9-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 850 and 0 Target number of residues in the AU: 850 Target solvent content: 0.5144 Checking the provided sequence file Detected sequence length: 258 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 516 Adjusted target solvent content: 0.71 Input MTZ file: 2a2m-1.9-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: 209 Cell parameters: 283.292 283.292 283.292 90.000 90.000 90.000 Input sequence file: 2a2m-1.9-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4128 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 1 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 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: 163.559 1.880 Wilson plot Bfac: 26.58 74702 reflections ( 94.58 % complete ) and 0 restraints for refining 4586 atoms. Observations/parameters ratio is 4.07 ------------------------------------------------------ Starting model: R = 0.3180 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2670 (Rfree = 0.000) for 4586 atoms. Found 187 (187 requested) and removed 90 (93 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.10 1.56 NCS extension: 0 residues added, 4683 seeds are put forward Round 1: 403 peptides, 36 chains. Longest chain 39 peptides. Score 0.626 Round 2: 439 peptides, 17 chains. Longest chain 69 peptides. Score 0.766 Round 3: 442 peptides, 10 chains. Longest chain 140 peptides. Score 0.800 Round 4: 445 peptides, 9 chains. Longest chain 114 peptides. Score 0.806 Round 5: 447 peptides, 13 chains. Longest chain 74 peptides. Score 0.790 Taking the results from Round 4 Chains 11, Residues 436, Estimated correctness of the model 97.1 % 8 chains (421 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 A and 69 A Built loop between residues 84 A and 87 A Built loop between residues 121 A and 124 A Built loop between residues 177 A and 181 A Built loop between residues 81 B and 84 B Built loop between residues 192 B and 198 B 3 chains (448 residues) following loop building 2 chains (438 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4430 restraints for refining 4414 atoms. 780 conditional restraints added. Observations/parameters ratio is 4.23 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2284 (Rfree = 0.000) for 4414 atoms. Found 180 (180 requested) and removed 60 (90 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2043 (Rfree = 0.000) for 4500 atoms. Found 185 (185 requested) and removed 38 (92 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1933 (Rfree = 0.000) for 4625 atoms. Found 189 (189 requested) and removed 56 (94 requested) atoms. Cycle 4: After refmac, R = 0.1875 (Rfree = 0.000) for 4743 atoms. Found 183 (194 requested) and removed 94 (97 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1840 (Rfree = 0.000) for 4811 atoms. Found 185 (193 requested) and removed 100 (98 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.03 1.51 NCS extension: 0 residues added (16 deleted due to clashes), 4896 seeds are put forward Round 1: 451 peptides, 3 chains. Longest chain 225 peptides. Score 0.836 Round 2: 446 peptides, 7 chains. Longest chain 151 peptides. Score 0.816 Round 3: 449 peptides, 5 chains. Longest chain 157 peptides. Score 0.826 Round 4: 445 peptides, 7 chains. Longest chain 128 peptides. Score 0.815 Round 5: 446 peptides, 6 chains. Longest chain 157 peptides. Score 0.820 Taking the results from Round 1 Chains 3, Residues 448, Estimated correctness of the model 97.9 % 3 chains (448 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 A and 190 A 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4285 restraints for refining 4451 atoms. 571 conditional restraints added. Observations/parameters ratio is 4.20 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1875 (Rfree = 0.000) for 4451 atoms. Found 174 (174 requested) and removed 28 (90 requested) atoms. Cycle 7: After refmac, R = 0.1811 (Rfree = 0.000) for 4585 atoms. Found 179 (180 requested) and removed 63 (93 requested) atoms. Cycle 8: After refmac, R = 0.1763 (Rfree = 0.000) for 4691 atoms. Found 184 (184 requested) and removed 83 (96 requested) atoms. Cycle 9: After refmac, R = 0.1747 (Rfree = 0.000) for 4777 atoms. Found 187 (187 requested) and removed 97 (97 requested) atoms. Cycle 10: After refmac, R = 0.1767 (Rfree = 0.000) for 4850 atoms. Found 173 (186 requested) and removed 111 (99 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4912 seeds are put forward Round 1: 451 peptides, 3 chains. Longest chain 226 peptides. Score 0.836 Round 2: 448 peptides, 6 chains. Longest chain 226 peptides. Score 0.821 Round 3: 451 peptides, 4 chains. Longest chain 214 peptides. Score 0.832 Round 4: 451 peptides, 3 chains. Longest chain 226 peptides. Score 0.836 Round 5: 446 peptides, 9 chains. Longest chain 150 peptides. Score 0.807 Taking the results from Round 4 Chains 3, Residues 448, Estimated correctness of the model 97.9 % 3 chains (448 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 B and 71 B 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4320 restraints for refining 4477 atoms. 602 conditional restraints added. Observations/parameters ratio is 4.17 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1962 (Rfree = 0.000) for 4477 atoms. Found 167 (167 requested) and removed 31 (91 requested) atoms. Cycle 12: After refmac, R = 0.1831 (Rfree = 0.000) for 4608 atoms. Found 148 (173 requested) and removed 51 (94 requested) atoms. Cycle 13: After refmac, R = 0.1770 (Rfree = 0.000) for 4688 atoms. Found 156 (177 requested) and removed 67 (96 requested) atoms. Cycle 14: After refmac, R = 0.1746 (Rfree = 0.000) for 4758 atoms. Found 179 (179 requested) and removed 69 (97 requested) atoms. Cycle 15: After refmac, R = 0.1751 (Rfree = 0.000) for 4848 atoms. Found 167 (182 requested) and removed 102 (99 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.03 1.51 NCS extension: 0 residues added, 4913 seeds are put forward Round 1: 453 peptides, 3 chains. Longest chain 226 peptides. Score 0.837 Round 2: 444 peptides, 6 chains. Longest chain 150 peptides. Score 0.819 Round 3: 446 peptides, 6 chains. Longest chain 138 peptides. Score 0.820 Round 4: 447 peptides, 7 chains. Longest chain 115 peptides. Score 0.816 Round 5: 443 peptides, 10 chains. Longest chain 112 peptides. Score 0.801 Taking the results from Round 1 Chains 3, Residues 450, Estimated correctness of the model 97.9 % 3 chains (450 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 B and 190 B 2 chains (452 residues) following loop building 2 chains (452 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4314 restraints for refining 4507 atoms. 581 conditional restraints added. Observations/parameters ratio is 4.14 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1829 (Rfree = 0.000) for 4507 atoms. Found 166 (166 requested) and removed 30 (92 requested) atoms. Cycle 17: After refmac, R = 0.1763 (Rfree = 0.000) for 4634 atoms. Found 170 (170 requested) and removed 58 (94 requested) atoms. Cycle 18: After refmac, R = 0.1750 (Rfree = 0.000) for 4734 atoms. Found 174 (174 requested) and removed 84 (96 requested) atoms. Cycle 19: After refmac, R = 0.1731 (Rfree = 0.000) for 4806 atoms. Found 177 (177 requested) and removed 90 (98 requested) atoms. Cycle 20: After refmac, R = 0.1713 (Rfree = 0.000) for 4872 atoms. Found 175 (175 requested) and removed 104 (99 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4943 seeds are put forward Round 1: 452 peptides, 2 chains. Longest chain 226 peptides. Score 0.840 Round 2: 446 peptides, 5 chains. Longest chain 152 peptides. Score 0.824 Round 3: 449 peptides, 5 chains. Longest chain 226 peptides. Score 0.826 Round 4: 449 peptides, 6 chains. Longest chain 130 peptides. Score 0.822 Round 5: 444 peptides, 8 chains. Longest chain 110 peptides. Score 0.810 Taking the results from Round 1 Chains 2, Residues 450, Estimated correctness of the model 98.0 % 2 chains (450 residues) have been docked in sequence Building loops using Loopy2018 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4352 restraints for refining 4530 atoms. 634 conditional restraints added. Observations/parameters ratio is 4.12 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1791 (Rfree = 0.000) for 4530 atoms. Found 159 (159 requested) and removed 20 (92 requested) atoms. Cycle 22: After refmac, R = 0.1755 (Rfree = 0.000) for 4648 atoms. Found 163 (163 requested) and removed 63 (95 requested) atoms. Cycle 23: After refmac, R = 0.1719 (Rfree = 0.000) for 4736 atoms. Found 165 (167 requested) and removed 49 (97 requested) atoms. Cycle 24: After refmac, R = 0.1712 (Rfree = 0.000) for 4841 atoms. Found 136 (170 requested) and removed 91 (99 requested) atoms. Cycle 25: After refmac, R = 0.1712 (Rfree = 0.000) for 4860 atoms. Found 166 (167 requested) and removed 90 (99 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4936 seeds are put forward Round 1: 449 peptides, 4 chains. Longest chain 226 peptides. Score 0.830 Round 2: 450 peptides, 3 chains. Longest chain 226 peptides. Score 0.835 Round 3: 449 peptides, 6 chains. Longest chain 151 peptides. Score 0.822 Round 4: 452 peptides, 9 chains. Longest chain 91 peptides. Score 0.812 Round 5: 446 peptides, 8 chains. Longest chain 88 peptides. Score 0.811 Taking the results from Round 2 Chains 3, Residues 447, Estimated correctness of the model 97.9 % 3 chains (447 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 117 B and 119 B 2 chains (448 residues) following loop building 2 chains (448 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4352 restraints for refining 4505 atoms. 646 conditional restraints added. Observations/parameters ratio is 4.15 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1828 (Rfree = 0.000) for 4505 atoms. Found 151 (151 requested) and removed 35 (92 requested) atoms. Cycle 27: After refmac, R = 0.1764 (Rfree = 0.000) for 4612 atoms. Found 154 (154 requested) and removed 38 (94 requested) atoms. Cycle 28: After refmac, R = 0.1726 (Rfree = 0.000) for 4716 atoms. Found 158 (158 requested) and removed 50 (96 requested) atoms. Cycle 29: After refmac, R = 0.1711 (Rfree = 0.000) for 4809 atoms. Found 162 (162 requested) and removed 68 (98 requested) atoms. Cycle 30: After refmac, R = 0.1699 (Rfree = 0.000) for 4888 atoms. Found 164 (164 requested) and removed 101 (100 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4952 seeds are put forward Round 1: 454 peptides, 3 chains. Longest chain 227 peptides. Score 0.838 Round 2: 449 peptides, 7 chains. Longest chain 152 peptides. Score 0.818 Round 3: 450 peptides, 4 chains. Longest chain 226 peptides. Score 0.831 Round 4: 447 peptides, 10 chains. Longest chain 91 peptides. Score 0.804 Round 5: 449 peptides, 8 chains. Longest chain 149 peptides. Score 0.814 Taking the results from Round 1 Chains 3, Residues 451, Estimated correctness of the model 97.9 % 3 chains (451 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 A and 190 A 2 chains (453 residues) following loop building 2 chains (453 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4323 restraints for refining 4529 atoms. 583 conditional restraints added. Observations/parameters ratio is 4.12 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1796 (Rfree = 0.000) for 4529 atoms. Found 148 (148 requested) and removed 29 (92 requested) atoms. Cycle 32: After refmac, R = 0.1735 (Rfree = 0.000) for 4635 atoms. Found 151 (151 requested) and removed 44 (94 requested) atoms. Cycle 33: After refmac, R = 0.1708 (Rfree = 0.000) for 4732 atoms. Found 154 (154 requested) and removed 63 (96 requested) atoms. Cycle 34: After refmac, R = 0.1692 (Rfree = 0.000) for 4810 atoms. Found 158 (158 requested) and removed 82 (98 requested) atoms. Cycle 35: After refmac, R = 0.1685 (Rfree = 0.000) for 4867 atoms. Found 155 (155 requested) and removed 88 (99 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4934 seeds are put forward Round 1: 451 peptides, 3 chains. Longest chain 226 peptides. Score 0.836 Round 2: 446 peptides, 6 chains. Longest chain 226 peptides. Score 0.820 Round 3: 450 peptides, 4 chains. Longest chain 159 peptides. Score 0.831 Round 4: 441 peptides, 9 chains. Longest chain 139 peptides. Score 0.803 Round 5: 446 peptides, 9 chains. Longest chain 110 peptides. Score 0.807 Taking the results from Round 1 Chains 3, Residues 448, Estimated correctness of the model 97.9 % 3 chains (448 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 A and 190 A 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4328 restraints for refining 4516 atoms. 610 conditional restraints added. Observations/parameters ratio is 4.14 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1795 (Rfree = 0.000) for 4516 atoms. Found 140 (140 requested) and removed 21 (92 requested) atoms. Cycle 37: After refmac, R = 0.1745 (Rfree = 0.000) for 4618 atoms. Found 144 (144 requested) and removed 48 (94 requested) atoms. Cycle 38: After refmac, R = 0.1707 (Rfree = 0.000) for 4703 atoms. Found 146 (146 requested) and removed 58 (96 requested) atoms. Cycle 39: After refmac, R = 0.1697 (Rfree = 0.000) for 4780 atoms. Found 148 (148 requested) and removed 67 (97 requested) atoms. Cycle 40: After refmac, R = 0.1681 (Rfree = 0.000) for 4836 atoms. Found 150 (150 requested) and removed 96 (99 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4890 seeds are put forward Round 1: 451 peptides, 3 chains. Longest chain 226 peptides. Score 0.836 Round 2: 446 peptides, 6 chains. Longest chain 226 peptides. Score 0.820 Round 3: 450 peptides, 4 chains. Longest chain 226 peptides. Score 0.831 Round 4: 448 peptides, 6 chains. Longest chain 179 peptides. Score 0.821 Round 5: 448 peptides, 9 chains. Longest chain 87 peptides. Score 0.809 Taking the results from Round 1 Chains 3, Residues 448, Estimated correctness of the model 97.9 % 3 chains (448 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 B and 190 B 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4367 restraints for refining 4536 atoms. 649 conditional restraints added. Observations/parameters ratio is 4.12 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1802 (Rfree = 0.000) for 4536 atoms. Found 137 (137 requested) and removed 24 (92 requested) atoms. Cycle 42: After refmac, R = 0.1743 (Rfree = 0.000) for 4631 atoms. Found 140 (140 requested) and removed 44 (94 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1705 (Rfree = 0.000) for 4713 atoms. Found 143 (143 requested) and removed 47 (96 requested) atoms. Cycle 44: After refmac, R = 0.1687 (Rfree = 0.000) for 4798 atoms. Found 145 (145 requested) and removed 64 (98 requested) atoms. Cycle 45: After refmac, R = 0.1679 (Rfree = 0.000) for 4855 atoms. Found 147 (147 requested) and removed 75 (99 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.03 1.51 NCS extension: 0 residues added, 4927 seeds are put forward Round 1: 449 peptides, 3 chains. Longest chain 226 peptides. Score 0.834 Round 2: 444 peptides, 6 chains. Longest chain 226 peptides. Score 0.819 Round 3: 448 peptides, 6 chains. Longest chain 116 peptides. Score 0.821 Round 4: 443 peptides, 9 chains. Longest chain 115 peptides. Score 0.805 Round 5: 449 peptides, 6 chains. Longest chain 151 peptides. Score 0.822 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 446, Estimated correctness of the model 97.8 % 3 chains (446 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 187 B and 190 B 2 chains (448 residues) following loop building 2 chains (448 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 74702 reflections ( 94.58 % complete ) and 3706 restraints for refining 3603 atoms. Observations/parameters ratio is 5.18 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2417 (Rfree = 0.000) for 3603 atoms. Found 106 (106 requested) and removed 0 (106 requested) atoms. Cycle 47: After refmac, R = 0.2212 (Rfree = 0.000) for 3603 atoms. Found 109 (109 requested) and removed 4 (75 requested) atoms. Cycle 48: After refmac, R = 0.2052 (Rfree = 0.000) for 3603 atoms. Found 112 (112 requested) and removed 1 (77 requested) atoms. Cycle 49: After refmac, R = 0.1933 (Rfree = 0.000) for 3603 atoms. TimeTaking 1344