Sun 23 Dec 23:53:57 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 2p7i-1.7-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-1.7-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-1.7-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-1.7-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/2p7i-1.7-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-1.7-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 ============================================================ Sun 23 Dec 23:54:01 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/2p7i-1.7-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-1.7-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 502 and 0 Target number of residues in the AU: 502 Target solvent content: 0.5030 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.50 Input MTZ file: 2p7i-1.7-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: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-1.7-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4000 target number of atoms Had to go as low as 0.30 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: 94.045 1.740 Wilson plot Bfac: 23.93 56831 reflections ( 99.96 % complete ) and 0 restraints for refining 4448 atoms. Observations/parameters ratio is 3.19 ------------------------------------------------------ Starting model: R = 0.3117 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2571 (Rfree = 0.000) for 4448 atoms. Found 150 (226 requested) and removed 132 (113 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.00 2.00 NCS extension: 0 residues added, 4466 seeds are put forward Round 1: 368 peptides, 27 chains. Longest chain 43 peptides. Score 0.799 Round 2: 412 peptides, 13 chains. Longest chain 80 peptides. Score 0.905 Round 3: 428 peptides, 5 chains. Longest chain 164 peptides. Score 0.941 Round 4: 422 peptides, 12 chains. Longest chain 85 peptides. Score 0.914 Round 5: 423 peptides, 7 chains. Longest chain 120 peptides. Score 0.932 Taking the results from Round 3 Chains 6, Residues 423, Estimated correctness of the model 99.7 % 5 chains (419 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 96 A and 100 A Built loop between residues 77 B and 88 B 4 chains (436 residues) following loop building 3 chains (432 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 3996 restraints for refining 3989 atoms. 446 conditional restraints added. Observations/parameters ratio is 3.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2624 (Rfree = 0.000) for 3989 atoms. Found 129 (203 requested) and removed 90 (101 requested) atoms. Cycle 2: After refmac, R = 0.2385 (Rfree = 0.000) for 4017 atoms. Found 90 (201 requested) and removed 24 (102 requested) atoms. Cycle 3: After refmac, R = 0.2129 (Rfree = 0.000) for 4071 atoms. Found 91 (203 requested) and removed 30 (103 requested) atoms. Cycle 4: After refmac, R = 0.1994 (Rfree = 0.000) for 4117 atoms. Found 84 (206 requested) and removed 23 (105 requested) atoms. Cycle 5: After refmac, R = 0.1913 (Rfree = 0.000) for 4165 atoms. Found 93 (208 requested) and removed 34 (106 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.97 1.97 NCS extension: 51 residues added (184 deleted due to clashes), 4276 seeds are put forward Round 1: 438 peptides, 6 chains. Longest chain 114 peptides. Score 0.942 Round 2: 442 peptides, 6 chains. Longest chain 165 peptides. Score 0.943 Round 3: 446 peptides, 5 chains. Longest chain 172 peptides. Score 0.948 Round 4: 445 peptides, 4 chains. Longest chain 177 peptides. Score 0.950 Round 5: 443 peptides, 7 chains. Longest chain 189 peptides. Score 0.941 Taking the results from Round 4 Chains 4, Residues 441, Estimated correctness of the model 99.8 % 4 chains (441 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 78 A and 87 A Built loop between residues 199 B and 202 B 2 chains (451 residues) following loop building 2 chains (451 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 56831 reflections ( 99.96 % complete ) and 3981 restraints for refining 4144 atoms. 280 conditional restraints added. Observations/parameters ratio is 3.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2118 (Rfree = 0.000) for 4144 atoms. Found 102 (207 requested) and removed 92 (105 requested) atoms. Cycle 7: After refmac, R = 0.1966 (Rfree = 0.000) for 4148 atoms. Found 87 (203 requested) and removed 35 (105 requested) atoms. Cycle 8: After refmac, R = 0.1878 (Rfree = 0.000) for 4194 atoms. Found 84 (204 requested) and removed 36 (106 requested) atoms. Cycle 9: After refmac, R = 0.1814 (Rfree = 0.000) for 4234 atoms. Found 85 (206 requested) and removed 46 (107 requested) atoms. Cycle 10: After refmac, R = 0.1783 (Rfree = 0.000) for 4267 atoms. Found 100 (204 requested) and removed 51 (108 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.96 1.96 NCS extension: 16 residues added (212 deleted due to clashes), 4338 seeds are put forward Round 1: 447 peptides, 6 chains. Longest chain 176 peptides. Score 0.945 Round 2: 448 peptides, 4 chains. Longest chain 171 peptides. Score 0.951 Round 3: 446 peptides, 6 chains. Longest chain 164 peptides. Score 0.945 Round 4: 443 peptides, 8 chains. Longest chain 173 peptides. Score 0.938 Round 5: 442 peptides, 10 chains. Longest chain 85 peptides. Score 0.931 Taking the results from Round 2 Chains 5, Residues 444, Estimated correctness of the model 99.8 % 4 chains (440 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 A and 88 A Built loop between residues 194 B and 197 B 3 chains (449 residues) following loop building 2 chains (445 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4047 restraints for refining 4156 atoms. 380 conditional restraints added. Observations/parameters ratio is 3.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2009 (Rfree = 0.000) for 4156 atoms. Found 132 (194 requested) and removed 82 (105 requested) atoms. Cycle 12: After refmac, R = 0.1902 (Rfree = 0.000) for 4202 atoms. Found 77 (193 requested) and removed 52 (107 requested) atoms. Cycle 13: After refmac, R = 0.1835 (Rfree = 0.000) for 4223 atoms. Found 101 (189 requested) and removed 50 (107 requested) atoms. Cycle 14: After refmac, R = 0.1804 (Rfree = 0.000) for 4269 atoms. Found 84 (191 requested) and removed 62 (108 requested) atoms. Cycle 15: After refmac, R = 0.1778 (Rfree = 0.000) for 4286 atoms. Found 97 (187 requested) and removed 60 (109 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.96 1.96 NCS extension: 19 residues added (204 deleted due to clashes), 4344 seeds are put forward Round 1: 449 peptides, 5 chains. Longest chain 177 peptides. Score 0.949 Round 2: 453 peptides, 2 chains. Longest chain 228 peptides. Score 0.958 Round 3: 449 peptides, 4 chains. Longest chain 208 peptides. Score 0.951 Round 4: 448 peptides, 6 chains. Longest chain 150 peptides. Score 0.945 Round 5: 440 peptides, 10 chains. Longest chain 101 peptides. Score 0.930 Taking the results from Round 2 Chains 3, Residues 451, Estimated correctness of the model 99.9 % 2 chains (448 residues) have been docked in sequence Building loops using Loopy2018 3 chains (451 residues) following loop building 2 chains (448 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4014 restraints for refining 4178 atoms. 327 conditional restraints added. Observations/parameters ratio is 3.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2004 (Rfree = 0.000) for 4178 atoms. Found 145 (178 requested) and removed 84 (106 requested) atoms. Cycle 17: After refmac, R = 0.1891 (Rfree = 0.000) for 4232 atoms. Found 91 (176 requested) and removed 55 (107 requested) atoms. Cycle 18: After refmac, R = 0.1818 (Rfree = 0.000) for 4262 atoms. Found 99 (174 requested) and removed 42 (108 requested) atoms. Cycle 19: After refmac, R = 0.1770 (Rfree = 0.000) for 4314 atoms. Found 87 (175 requested) and removed 49 (109 requested) atoms. Cycle 20: After refmac, R = 0.1748 (Rfree = 0.000) for 4342 atoms. Found 100 (172 requested) and removed 59 (110 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.96 1.96 NCS extension: 20 residues added (206 deleted due to clashes), 4407 seeds are put forward Round 1: 449 peptides, 5 chains. Longest chain 177 peptides. Score 0.949 Round 2: 451 peptides, 3 chains. Longest chain 228 peptides. Score 0.955 Round 3: 447 peptides, 6 chains. Longest chain 165 peptides. Score 0.945 Round 4: 442 peptides, 7 chains. Longest chain 186 peptides. Score 0.940 Round 5: 450 peptides, 4 chains. Longest chain 198 peptides. Score 0.952 Taking the results from Round 2 Chains 4, Residues 448, Estimated correctness of the model 99.8 % 3 chains (445 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 194 B and 197 B 3 chains (450 residues) following loop building 2 chains (447 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4024 restraints for refining 4196 atoms. 345 conditional restraints added. Observations/parameters ratio is 3.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2006 (Rfree = 0.000) for 4196 atoms. Found 136 (162 requested) and removed 79 (106 requested) atoms. Cycle 22: After refmac, R = 0.1877 (Rfree = 0.000) for 4245 atoms. Found 112 (160 requested) and removed 38 (108 requested) atoms. Cycle 23: After refmac, R = 0.1824 (Rfree = 0.000) for 4315 atoms. Found 73 (162 requested) and removed 50 (109 requested) atoms. Cycle 24: After refmac, R = 0.1776 (Rfree = 0.000) for 4331 atoms. Found 79 (158 requested) and removed 47 (110 requested) atoms. Cycle 25: After refmac, R = 0.1763 (Rfree = 0.000) for 4360 atoms. Found 81 (155 requested) and removed 63 (111 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.96 1.96 NCS extension: 19 residues added (206 deleted due to clashes), 4400 seeds are put forward Round 1: 448 peptides, 5 chains. Longest chain 177 peptides. Score 0.948 Round 2: 450 peptides, 3 chains. Longest chain 224 peptides. Score 0.955 Round 3: 450 peptides, 5 chains. Longest chain 177 peptides. Score 0.949 Round 4: 447 peptides, 6 chains. Longest chain 104 peptides. Score 0.945 Round 5: 449 peptides, 5 chains. Longest chain 161 peptides. Score 0.949 Taking the results from Round 2 Chains 4, Residues 447, Estimated correctness of the model 99.8 % 3 chains (443 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 A and 88 A 3 chains (450 residues) following loop building 2 chains (446 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4047 restraints for refining 4220 atoms. 368 conditional restraints added. Observations/parameters ratio is 3.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2021 (Rfree = 0.000) for 4220 atoms. Found 146 (146 requested) and removed 83 (107 requested) atoms. Cycle 27: After refmac, R = 0.1920 (Rfree = 0.000) for 4272 atoms. Found 90 (144 requested) and removed 56 (109 requested) atoms. Cycle 28: After refmac, R = 0.1846 (Rfree = 0.000) for 4298 atoms. Found 89 (140 requested) and removed 49 (109 requested) atoms. Cycle 29: After refmac, R = 0.1795 (Rfree = 0.000) for 4336 atoms. Found 107 (136 requested) and removed 58 (110 requested) atoms. Cycle 30: After refmac, R = 0.1787 (Rfree = 0.000) for 4382 atoms. Found 106 (134 requested) and removed 73 (111 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.95 1.95 NCS extension: 21 residues added (237 deleted due to clashes), 4437 seeds are put forward Round 1: 449 peptides, 4 chains. Longest chain 224 peptides. Score 0.951 Round 2: 447 peptides, 5 chains. Longest chain 164 peptides. Score 0.948 Round 3: 448 peptides, 5 chains. Longest chain 164 peptides. Score 0.948 Round 4: 449 peptides, 6 chains. Longest chain 177 peptides. Score 0.946 Round 5: 448 peptides, 5 chains. Longest chain 172 peptides. Score 0.948 Taking the results from Round 1 Chains 6, Residues 445, Estimated correctness of the model 99.8 % 4 chains (441 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 B and 88 B Built loop between residues 196 B and 201 B 3 chains (450 residues) following loop building 2 chains (449 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4029 restraints for refining 4236 atoms. 342 conditional restraints added. Observations/parameters ratio is 3.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2011 (Rfree = 0.000) for 4236 atoms. Found 125 (125 requested) and removed 76 (107 requested) atoms. Cycle 32: After refmac, R = 0.1908 (Rfree = 0.000) for 4274 atoms. Found 122 (122 requested) and removed 55 (109 requested) atoms. Cycle 33: After refmac, R = 0.1832 (Rfree = 0.000) for 4338 atoms. Found 97 (124 requested) and removed 67 (110 requested) atoms. Cycle 34: After refmac, R = 0.1785 (Rfree = 0.000) for 4360 atoms. Found 100 (120 requested) and removed 66 (111 requested) atoms. Cycle 35: After refmac, R = 0.1768 (Rfree = 0.000) for 4384 atoms. Found 106 (116 requested) and removed 64 (111 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.95 1.95 NCS extension: 57 residues added (176 deleted due to clashes), 4486 seeds are put forward Round 1: 445 peptides, 6 chains. Longest chain 177 peptides. Score 0.944 Round 2: 449 peptides, 4 chains. Longest chain 189 peptides. Score 0.951 Round 3: 448 peptides, 4 chains. Longest chain 189 peptides. Score 0.951 Round 4: 442 peptides, 9 chains. Longest chain 127 peptides. Score 0.934 Round 5: 442 peptides, 9 chains. Longest chain 130 peptides. Score 0.934 Taking the results from Round 3 Chains 5, Residues 444, Estimated correctness of the model 99.8 % 4 chains (441 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 91 A and 94 A Built loop between residues 211 B and 216 B 3 chains (450 residues) following loop building 2 chains (447 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4032 restraints for refining 4226 atoms. 353 conditional restraints added. Observations/parameters ratio is 3.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2009 (Rfree = 0.000) for 4226 atoms. Found 107 (107 requested) and removed 65 (107 requested) atoms. Cycle 37: After refmac, R = 0.1889 (Rfree = 0.000) for 4256 atoms. Found 105 (108 requested) and removed 43 (108 requested) atoms. Cycle 38: After refmac, R = 0.1818 (Rfree = 0.000) for 4314 atoms. Found 99 (109 requested) and removed 47 (109 requested) atoms. Cycle 39: After refmac, R = 0.1782 (Rfree = 0.000) for 4365 atoms. Found 91 (111 requested) and removed 56 (111 requested) atoms. Cycle 40: After refmac, R = 0.1754 (Rfree = 0.000) for 4394 atoms. Found 110 (112 requested) and removed 69 (112 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.95 1.95 NCS extension: 0 residues added, 4435 seeds are put forward Round 1: 449 peptides, 5 chains. Longest chain 177 peptides. Score 0.949 Round 2: 451 peptides, 4 chains. Longest chain 229 peptides. Score 0.952 Round 3: 448 peptides, 6 chains. Longest chain 158 peptides. Score 0.945 Round 4: 445 peptides, 10 chains. Longest chain 76 peptides. Score 0.932 Round 5: 447 peptides, 5 chains. Longest chain 123 peptides. Score 0.948 Taking the results from Round 2 Chains 5, Residues 447, Estimated correctness of the model 99.8 % 4 chains (443 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 B and 87 B Built loop between residues 194 B and 197 B 3 chains (451 residues) following loop building 2 chains (447 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4039 restraints for refining 4238 atoms. 352 conditional restraints added. Observations/parameters ratio is 3.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1974 (Rfree = 0.000) for 4238 atoms. Found 107 (107 requested) and removed 76 (107 requested) atoms. Cycle 42: After refmac, R = 0.1865 (Rfree = 0.000) for 4262 atoms. Found 105 (108 requested) and removed 40 (108 requested) atoms. Cycle 43: After refmac, R = 0.1803 (Rfree = 0.000) for 4321 atoms. Found 100 (110 requested) and removed 59 (110 requested) atoms. Cycle 44: After refmac, R = 0.1770 (Rfree = 0.000) for 4358 atoms. Found 93 (111 requested) and removed 51 (111 requested) atoms. Cycle 45: After refmac, R = 0.1748 (Rfree = 0.000) for 4397 atoms. Found 77 (112 requested) and removed 64 (112 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.96 1.96 NCS extension: 49 residues added (176 deleted due to clashes), 4460 seeds are put forward Round 1: 448 peptides, 5 chains. Longest chain 177 peptides. Score 0.948 Round 2: 453 peptides, 2 chains. Longest chain 229 peptides. Score 0.958 Round 3: 448 peptides, 6 chains. Longest chain 165 peptides. Score 0.945 Round 4: 450 peptides, 4 chains. Longest chain 177 peptides. Score 0.952 Round 5: 452 peptides, 3 chains. Longest chain 229 peptides. Score 0.955 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 451, Estimated correctness of the model 99.9 % 2 chains (447 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 3 chains (451 residues) following loop building 2 chains (447 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 56831 reflections ( 99.96 % complete ) and 3687 restraints for refining 3604 atoms. Observations/parameters ratio is 3.94 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2512 (Rfree = 0.000) for 3604 atoms. Found 91 (91 requested) and removed 0 (91 requested) atoms. Cycle 47: After refmac, R = 0.2271 (Rfree = 0.000) for 3604 atoms. Found 94 (94 requested) and removed 0 (94 requested) atoms. Cycle 48: After refmac, R = 0.2046 (Rfree = 0.000) for 3604 atoms. Found 50 (96 requested) and removed 7 (96 requested) atoms. Cycle 49: After refmac, R = 0.1942 (Rfree = 0.000) for 3604 atoms. TimeTaking 68.65