Mon 24 Dec 07:37:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aam-2.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aam-2.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aam-2.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-2.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2aam-2.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-2.2-parrot-noncs ############### 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 07:37:29 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/noncs/ArpWArp/wArpResults/WorkingDir/2aam-2.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-2.2-parrot-noncs/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 4864 and 0 Target number of residues in the AU: 4864 Target solvent content: 0.5279 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 309 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1854 Adjusted target solvent content: 0.82 Input MTZ file: 2aam-2.2-parrot-noncs.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: 4 Cell parameters: 195.000 84.610 194.910 90.000 119.891 90.000 Input sequence file: 2aam-2.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.45 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. 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: 169.060 2.201 Wilson plot Bfac: 29.76 272043 reflections ( 97.42 % complete ) and 0 restraints for refining 16754 atoms. Observations/parameters ratio is 4.06 ------------------------------------------------------ Starting model: R = 0.3743 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3379 (Rfree = 0.000) for 16754 atoms. Found 436 (436 requested) and removed 219 (218 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.39 1.44 NCS extension: 0 residues added, 16971 seeds are put forward Round 1: 1445 peptides, 181 chains. Longest chain 35 peptides. Score 0.431 Round 2: 1503 peptides, 150 chains. Longest chain 32 peptides. Score 0.490 Round 3: 1501 peptides, 136 chains. Longest chain 39 peptides. Score 0.508 Round 4: 1508 peptides, 129 chains. Longest chain 47 peptides. Score 0.520 Round 5: 1555 peptides, 128 chains. Longest chain 50 peptides. Score 0.533 Taking the results from Round 5 Chains 145, Residues 1427, Estimated correctness of the model 76.1 % 33 chains (711 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 8796 restraints for refining 17748 atoms. Observations/parameters ratio is 3.83 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3325 (Rfree = 0.000) for 17748 atoms. Found 462 (462 requested) and removed 235 (231 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.3046 (Rfree = 0.000) for 17975 atoms. Found 468 (468 requested) and removed 155 (234 requested) atoms. Cycle 3: After refmac, R = 0.2927 (Rfree = 0.000) for 18288 atoms. Found 476 (476 requested) and removed 96 (238 requested) atoms. Cycle 4: After refmac, R = 0.2774 (Rfree = 0.000) for 18668 atoms. Found 474 (486 requested) and removed 128 (243 requested) atoms. Cycle 5: After refmac, R = 0.2666 (Rfree = 0.000) for 19014 atoms. Found 330 (495 requested) and removed 138 (247 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.27 1.37 NCS extension: 288 residues added (187 deleted due to clashes), 19529 seeds are put forward Round 1: 1606 peptides, 113 chains. Longest chain 68 peptides. Score 0.565 Round 2: 1620 peptides, 86 chains. Longest chain 92 peptides. Score 0.602 Round 3: 1623 peptides, 71 chains. Longest chain 71 peptides. Score 0.621 Round 4: 1614 peptides, 73 chains. Longest chain 102 peptides. Score 0.616 Round 5: 1624 peptides, 77 chains. Longest chain 131 peptides. Score 0.614 Taking the results from Round 3 Chains 90, Residues 1552, Estimated correctness of the model 83.7 % 42 chains (1258 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 11799 restraints for refining 18916 atoms. Observations/parameters ratio is 3.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2944 (Rfree = 0.000) for 18916 atoms. Found 493 (493 requested) and removed 263 (246 requested) atoms. Cycle 7: After refmac, R = 0.2711 (Rfree = 0.000) for 19146 atoms. Found 499 (499 requested) and removed 249 (249 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2585 (Rfree = 0.000) for 19396 atoms. Found 494 (505 requested) and removed 233 (252 requested) atoms. Cycle 9: After refmac, R = 0.2486 (Rfree = 0.000) for 19657 atoms. Found 415 (512 requested) and removed 225 (256 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2430 (Rfree = 0.000) for 19847 atoms. Found 354 (517 requested) and removed 271 (258 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.25 1.36 NCS extension: 140 residues added (551 deleted due to clashes), 20090 seeds are put forward Round 1: 1644 peptides, 58 chains. Longest chain 112 peptides. Score 0.641 Round 2: 1655 peptides, 43 chains. Longest chain 129 peptides. Score 0.661 Round 3: 1666 peptides, 35 chains. Longest chain 148 peptides. Score 0.672 Round 4: 1656 peptides, 39 chains. Longest chain 241 peptides. Score 0.665 Round 5: 1640 peptides, 47 chains. Longest chain 129 peptides. Score 0.653 Taking the results from Round 3 Chains 42, Residues 1631, Estimated correctness of the model 87.5 % 25 chains (1472 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13166 restraints for refining 18648 atoms. Observations/parameters ratio is 3.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2664 (Rfree = 0.000) for 18648 atoms. Found 486 (486 requested) and removed 157 (243 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2460 (Rfree = 0.000) for 18977 atoms. Found 494 (494 requested) and removed 203 (247 requested) atoms. Cycle 13: After refmac, R = 0.2355 (Rfree = 0.000) for 19268 atoms. Found 463 (502 requested) and removed 191 (251 requested) atoms. Cycle 14: After refmac, R = 0.2294 (Rfree = 0.000) for 19540 atoms. Found 414 (509 requested) and removed 172 (254 requested) atoms. Cycle 15: After refmac, R = 0.2245 (Rfree = 0.000) for 19782 atoms. Found 366 (515 requested) and removed 189 (257 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.24 1.35 NCS extension: 122 residues added (1079 deleted due to clashes), 20087 seeds are put forward Round 1: 1673 peptides, 26 chains. Longest chain 272 peptides. Score 0.683 Round 2: 1699 peptides, 24 chains. Longest chain 252 peptides. Score 0.691 Round 3: 1687 peptides, 29 chains. Longest chain 231 peptides. Score 0.683 Round 4: 1680 peptides, 26 chains. Longest chain 202 peptides. Score 0.685 Round 5: 1667 peptides, 41 chains. Longest chain 143 peptides. Score 0.665 Taking the results from Round 2 Chains 29, Residues 1675, Estimated correctness of the model 88.8 % 14 chains (1564 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13763 restraints for refining 18832 atoms. Observations/parameters ratio is 3.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2478 (Rfree = 0.000) for 18832 atoms. Found 491 (491 requested) and removed 123 (245 requested) atoms. Cycle 17: After refmac, R = 0.2327 (Rfree = 0.000) for 19200 atoms. Found 500 (500 requested) and removed 124 (250 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2260 (Rfree = 0.000) for 19576 atoms. Found 393 (510 requested) and removed 159 (255 requested) atoms. Cycle 19: After refmac, R = 0.2217 (Rfree = 0.000) for 19810 atoms. Found 345 (516 requested) and removed 175 (258 requested) atoms. Cycle 20: After refmac, R = 0.2187 (Rfree = 0.000) for 19980 atoms. Found 343 (520 requested) and removed 279 (260 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.24 1.35 NCS extension: 358 residues added (2093 deleted due to clashes), 20404 seeds are put forward Round 1: 1686 peptides, 25 chains. Longest chain 278 peptides. Score 0.687 Round 2: 1684 peptides, 30 chains. Longest chain 203 peptides. Score 0.681 Round 3: 1695 peptides, 30 chains. Longest chain 219 peptides. Score 0.683 Round 4: 1681 peptides, 34 chains. Longest chain 184 peptides. Score 0.676 Round 5: 1673 peptides, 36 chains. Longest chain 162 peptides. Score 0.672 Taking the results from Round 1 Chains 26, Residues 1661, Estimated correctness of the model 88.5 % 15 chains (1615 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13925 restraints for refining 18803 atoms. Observations/parameters ratio is 3.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2311 (Rfree = 0.000) for 18803 atoms. Found 490 (490 requested) and removed 160 (245 requested) atoms. Cycle 22: After refmac, R = 0.2232 (Rfree = 0.000) for 19133 atoms. Found 498 (498 requested) and removed 167 (249 requested) atoms. Cycle 23: After refmac, R = 0.2190 (Rfree = 0.000) for 19464 atoms. Found 430 (507 requested) and removed 271 (253 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2161 (Rfree = 0.000) for 19623 atoms. Found 429 (511 requested) and removed 199 (255 requested) atoms. Cycle 25: After refmac, R = 0.2132 (Rfree = 0.000) for 19853 atoms. Found 356 (517 requested) and removed 216 (258 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.24 1.35 NCS extension: 139 residues added (1544 deleted due to clashes), 20138 seeds are put forward Round 1: 1678 peptides, 28 chains. Longest chain 147 peptides. Score 0.682 Round 2: 1672 peptides, 22 chains. Longest chain 216 peptides. Score 0.688 Round 3: 1678 peptides, 29 chains. Longest chain 253 peptides. Score 0.681 Round 4: 1686 peptides, 30 chains. Longest chain 215 peptides. Score 0.681 Round 5: 1670 peptides, 40 chains. Longest chain 160 peptides. Score 0.667 Taking the results from Round 2 Chains 25, Residues 1650, Estimated correctness of the model 88.6 % 18 chains (1614 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 272043 reflections ( 97.42 % complete ) and 13869 restraints for refining 18872 atoms. Observations/parameters ratio is 3.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2266 (Rfree = 0.000) for 18872 atoms. Found 492 (492 requested) and removed 97 (246 requested) atoms. Cycle 27: After refmac, R = 0.2192 (Rfree = 0.000) for 19267 atoms. Found 466 (502 requested) and removed 135 (251 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2147 (Rfree = 0.000) for 19598 atoms. Found 374 (511 requested) and removed 220 (255 requested) atoms. Cycle 29: After refmac, R = 0.2119 (Rfree = 0.000) for 19752 atoms. Found 373 (515 requested) and removed 246 (257 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2102 (Rfree = 0.000) for 19879 atoms. Found 355 (518 requested) and removed 226 (259 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.24 1.35 NCS extension: 52 residues added (1280 deleted due to clashes), 20065 seeds are put forward Round 1: 1666 peptides, 20 chains. Longest chain 206 peptides. Score 0.689 Round 2: 1675 peptides, 20 chains. Longest chain 269 peptides. Score 0.691 Round 3: 1667 peptides, 24 chains. Longest chain 282 peptides. Score 0.685 Round 4: 1662 peptides, 29 chains. Longest chain 154 peptides. Score 0.678 Round 5: 1660 peptides, 28 chains. Longest chain 249 peptides. Score 0.679 Taking the results from Round 2 Chains 23, Residues 1655, Estimated correctness of the model 88.8 % 13 chains (1548 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13644 restraints for refining 18958 atoms. Observations/parameters ratio is 3.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2347 (Rfree = 0.000) for 18958 atoms. Found 494 (494 requested) and removed 90 (247 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2207 (Rfree = 0.000) for 19362 atoms. Found 504 (504 requested) and removed 198 (252 requested) atoms. Cycle 33: After refmac, R = 0.2153 (Rfree = 0.000) for 19668 atoms. Found 390 (512 requested) and removed 231 (256 requested) atoms. Cycle 34: After refmac, R = 0.2119 (Rfree = 0.000) for 19827 atoms. Found 402 (516 requested) and removed 140 (258 requested) atoms. Cycle 35: After refmac, R = 0.2092 (Rfree = 0.000) for 20089 atoms. Found 274 (523 requested) and removed 188 (261 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.24 1.35 NCS extension: 165 residues added (1804 deleted due to clashes), 20341 seeds are put forward Round 1: 1683 peptides, 18 chains. Longest chain 280 peptides. Score 0.694 Round 2: 1673 peptides, 18 chains. Longest chain 279 peptides. Score 0.692 Round 3: 1678 peptides, 20 chains. Longest chain 282 peptides. Score 0.691 Round 4: 1668 peptides, 25 chains. Longest chain 252 peptides. Score 0.684 Round 5: 1647 peptides, 36 chains. Longest chain 143 peptides. Score 0.667 Taking the results from Round 1 Chains 19, Residues 1665, Estimated correctness of the model 89.0 % 11 chains (1628 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13998 restraints for refining 19147 atoms. Observations/parameters ratio is 3.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2219 (Rfree = 0.000) for 19147 atoms. Found 499 (499 requested) and removed 99 (249 requested) atoms. Cycle 37: After refmac, R = 0.2157 (Rfree = 0.000) for 19547 atoms. Found 428 (509 requested) and removed 119 (254 requested) atoms. Cycle 38: After refmac, R = 0.2119 (Rfree = 0.000) for 19856 atoms. Found 358 (517 requested) and removed 155 (258 requested) atoms. Cycle 39: After refmac, R = 0.2091 (Rfree = 0.000) for 20059 atoms. Found 300 (523 requested) and removed 235 (261 requested) atoms. Cycle 40: After refmac, R = 0.2077 (Rfree = 0.000) for 20124 atoms. Found 335 (524 requested) and removed 192 (262 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.23 1.35 NCS extension: 55 residues added (1075 deleted due to clashes), 20322 seeds are put forward Round 1: 1680 peptides, 17 chains. Longest chain 275 peptides. Score 0.695 Round 2: 1677 peptides, 23 chains. Longest chain 282 peptides. Score 0.688 Round 3: 1675 peptides, 20 chains. Longest chain 282 peptides. Score 0.691 Round 4: 1679 peptides, 24 chains. Longest chain 251 peptides. Score 0.687 Round 5: 1654 peptides, 34 chains. Longest chain 135 peptides. Score 0.671 Taking the results from Round 1 Chains 19, Residues 1663, Estimated correctness of the model 89.0 % 12 chains (1634 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 14009 restraints for refining 19153 atoms. Observations/parameters ratio is 3.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2204 (Rfree = 0.000) for 19153 atoms. Found 499 (499 requested) and removed 70 (249 requested) atoms. Cycle 42: After refmac, R = 0.2135 (Rfree = 0.000) for 19582 atoms. Found 484 (510 requested) and removed 111 (255 requested) atoms. Cycle 43: After refmac, R = 0.2101 (Rfree = 0.000) for 19955 atoms. Found 326 (520 requested) and removed 190 (260 requested) atoms. Cycle 44: After refmac, R = 0.2075 (Rfree = 0.000) for 20091 atoms. Found 332 (523 requested) and removed 204 (261 requested) atoms. Cycle 45: After refmac, R = 0.2060 (Rfree = 0.000) for 20219 atoms. Found 333 (527 requested) and removed 247 (263 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.23 1.35 NCS extension: 135 residues added (2374 deleted due to clashes), 20440 seeds are put forward Round 1: 1674 peptides, 19 chains. Longest chain 277 peptides. Score 0.691 Round 2: 1669 peptides, 19 chains. Longest chain 282 peptides. Score 0.691 Round 3: 1667 peptides, 24 chains. Longest chain 282 peptides. Score 0.685 Round 4: 1664 peptides, 25 chains. Longest chain 154 peptides. Score 0.683 Round 5: 1660 peptides, 27 chains. Longest chain 224 peptides. Score 0.680 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 1650, Estimated correctness of the model 88.8 % 15 chains (1626 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 35 A and 40 A Built loop between residues 89 A and 92 A Built loop between residues 143 A and 148 A Built loop between residues 49 C and 52 C Built loop between residues 147 C and 150 C Built loop between residues 134 B and 144 B Built loop between residues 60 F and 69 F Built loop between residues 113 F and 120 F Built loop between residues 147 F and 150 F 9 chains (1676 residues) following loop building 6 chains (1665 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 272043 reflections ( 97.42 % complete ) and 14203 restraints for refining 13836 atoms. Observations/parameters ratio is 4.92 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2712 (Rfree = 0.000) for 13836 atoms. Found 360 (360 requested) and removed 0 (360 requested) atoms. Cycle 47: After refmac, R = 0.2562 (Rfree = 0.000) for 13836 atoms. Found 136 (370 requested) and removed 4 (185 requested) atoms. Cycle 48: After refmac, R = 0.2489 (Rfree = 0.000) for 13836 atoms. Found 79 (373 requested) and removed 12 (186 requested) atoms. Cycle 49: After refmac, R = 0.2449 (Rfree = 0.000) for 13836 atoms. Found 52 (375 requested) and removed 13 (187 requested) atoms. Writing output files ... TimeTaking 283.07