null Mon 24 Dec 00:04:26 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 2aam-2.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-2.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-2.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-2.2-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/2aam-2.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-2.2-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 00:04:31 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/2aam-2.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-2.2-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 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-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: 4 Cell parameters: 195.000 84.610 194.910 90.000 119.891 90.000 Input sequence file: 2aam-2.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.25 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 16828 atoms. Observations/parameters ratio is 4.04 ------------------------------------------------------ Starting model: R = 0.3591 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3149 (Rfree = 0.000) for 16828 atoms. Found 438 (438 requested) and removed 225 (219 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.37 1.43 NCS extension: 0 residues added, 17041 seeds are put forward Round 1: 1492 peptides, 143 chains. Longest chain 34 peptides. Score 0.496 Round 2: 1555 peptides, 109 chains. Longest chain 61 peptides. Score 0.558 Round 3: 1578 peptides, 87 chains. Longest chain 63 peptides. Score 0.591 Round 4: 1599 peptides, 68 chains. Longest chain 113 peptides. Score 0.619 Round 5: 1601 peptides, 72 chains. Longest chain 82 peptides. Score 0.615 Taking the results from Round 4 Chains 84, Residues 1531, Estimated correctness of the model 83.5 % 43 chains (1328 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 12058 restraints for refining 16804 atoms. Observations/parameters ratio is 4.05 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3063 (Rfree = 0.000) for 16804 atoms. Found 438 (438 requested) and removed 243 (219 requested) atoms. Cycle 2: After refmac, R = 0.2818 (Rfree = 0.000) for 16999 atoms. Found 443 (443 requested) and removed 177 (221 requested) atoms. Cycle 3: After refmac, R = 0.2674 (Rfree = 0.000) for 17265 atoms. Found 450 (450 requested) and removed 204 (225 requested) atoms. Cycle 4: After refmac, R = 0.2573 (Rfree = 0.000) for 17511 atoms. Found 456 (456 requested) and removed 172 (228 requested) atoms. Cycle 5: After refmac, R = 0.2488 (Rfree = 0.000) for 17795 atoms. Found 464 (464 requested) and removed 206 (232 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.24 1.35 NCS extension: 235 residues added (706 deleted due to clashes), 18308 seeds are put forward Round 1: 1648 peptides, 39 chains. Longest chain 222 peptides. Score 0.664 Round 2: 1662 peptides, 30 chains. Longest chain 257 peptides. Score 0.677 Round 3: 1659 peptides, 37 chains. Longest chain 133 peptides. Score 0.668 Round 4: 1674 peptides, 35 chains. Longest chain 191 peptides. Score 0.673 Round 5: 1659 peptides, 43 chains. Longest chain 151 peptides. Score 0.661 Taking the results from Round 2 Chains 40, Residues 1632, Estimated correctness of the model 87.8 % 21 chains (1494 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13254 restraints for refining 16905 atoms. Observations/parameters ratio is 4.02 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2657 (Rfree = 0.000) for 16905 atoms. Found 440 (440 requested) and removed 83 (220 requested) atoms. Cycle 7: After refmac, R = 0.2543 (Rfree = 0.000) for 17262 atoms. Found 450 (450 requested) and removed 41 (225 requested) atoms. Cycle 8: After refmac, R = 0.2474 (Rfree = 0.000) for 17671 atoms. Found 460 (460 requested) and removed 53 (230 requested) atoms. Cycle 9: After refmac, R = 0.2409 (Rfree = 0.000) for 18078 atoms. Found 375 (471 requested) and removed 118 (235 requested) atoms. Cycle 10: After refmac, R = 0.2365 (Rfree = 0.000) for 18335 atoms. Found 360 (478 requested) and removed 90 (239 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.24 1.35 NCS extension: 279 residues added (2270 deleted due to clashes), 18887 seeds are put forward Round 1: 1669 peptides, 22 chains. Longest chain 240 peptides. Score 0.687 Round 2: 1663 peptides, 26 chains. Longest chain 205 peptides. Score 0.682 Round 3: 1664 peptides, 31 chains. Longest chain 156 peptides. Score 0.676 Round 4: 1647 peptides, 35 chains. Longest chain 200 peptides. Score 0.668 Round 5: 1634 peptides, 35 chains. Longest chain 152 peptides. Score 0.666 Taking the results from Round 1 Chains 24, Residues 1647, Estimated correctness of the model 88.5 % 17 chains (1616 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13841 restraints for refining 17651 atoms. Observations/parameters ratio is 3.85 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2513 (Rfree = 0.000) for 17651 atoms. Found 460 (460 requested) and removed 74 (230 requested) atoms. Cycle 12: After refmac, R = 0.2370 (Rfree = 0.000) for 18037 atoms. Found 470 (470 requested) and removed 87 (235 requested) atoms. Cycle 13: After refmac, R = 0.2297 (Rfree = 0.000) for 18420 atoms. Found 375 (480 requested) and removed 112 (240 requested) atoms. Cycle 14: After refmac, R = 0.2249 (Rfree = 0.000) for 18683 atoms. Found 369 (487 requested) and removed 110 (243 requested) atoms. Cycle 15: After refmac, R = 0.2213 (Rfree = 0.000) for 18942 atoms. Found 332 (493 requested) and removed 140 (246 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.24 1.35 NCS extension: 79 residues added (1844 deleted due to clashes), 19214 seeds are put forward Round 1: 1690 peptides, 22 chains. Longest chain 277 peptides. Score 0.691 Round 2: 1696 peptides, 26 chains. Longest chain 257 peptides. Score 0.688 Round 3: 1686 peptides, 28 chains. Longest chain 224 peptides. Score 0.684 Round 4: 1664 peptides, 37 chains. Longest chain 151 peptides. Score 0.669 Round 5: 1683 peptides, 31 chains. Longest chain 258 peptides. Score 0.680 Taking the results from Round 1 Chains 22, Residues 1668, Estimated correctness of the model 88.8 % 13 chains (1627 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13989 restraints for refining 18068 atoms. Observations/parameters ratio is 3.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2398 (Rfree = 0.000) for 18068 atoms. Found 471 (471 requested) and removed 69 (235 requested) atoms. Cycle 17: After refmac, R = 0.2265 (Rfree = 0.000) for 18470 atoms. Found 481 (481 requested) and removed 191 (240 requested) atoms. Cycle 18: After refmac, R = 0.2215 (Rfree = 0.000) for 18760 atoms. Found 473 (489 requested) and removed 251 (244 requested) atoms. Cycle 19: After refmac, R = 0.2184 (Rfree = 0.000) for 18982 atoms. Found 432 (494 requested) and removed 214 (247 requested) atoms. Cycle 20: After refmac, R = 0.2161 (Rfree = 0.000) for 19200 atoms. Found 382 (500 requested) and removed 200 (250 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.23 1.35 NCS extension: 13 residues added (768 deleted due to clashes), 19398 seeds are put forward Round 1: 1687 peptides, 22 chains. Longest chain 281 peptides. Score 0.691 Round 2: 1688 peptides, 24 chains. Longest chain 278 peptides. Score 0.688 Round 3: 1682 peptides, 30 chains. Longest chain 210 peptides. Score 0.681 Round 4: 1676 peptides, 29 chains. Longest chain 258 peptides. Score 0.681 Round 5: 1665 peptides, 36 chains. Longest chain 133 peptides. Score 0.671 Taking the results from Round 1 Chains 22, Residues 1665, Estimated correctness of the model 88.8 % 16 chains (1642 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 14031 restraints for refining 18187 atoms. Observations/parameters ratio is 3.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2354 (Rfree = 0.000) for 18187 atoms. Found 474 (474 requested) and removed 47 (237 requested) atoms. Cycle 22: After refmac, R = 0.2235 (Rfree = 0.000) for 18614 atoms. Found 485 (485 requested) and removed 97 (242 requested) atoms. Cycle 23: After refmac, R = 0.2185 (Rfree = 0.000) for 19002 atoms. Found 361 (495 requested) and removed 134 (247 requested) atoms. Cycle 24: After refmac, R = 0.2150 (Rfree = 0.000) for 19229 atoms. Found 329 (501 requested) and removed 141 (250 requested) atoms. Cycle 25: After refmac, R = 0.2126 (Rfree = 0.000) for 19417 atoms. Found 289 (506 requested) and removed 172 (253 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.23 1.35 NCS extension: 27 residues added (825 deleted due to clashes), 19562 seeds are put forward Round 1: 1672 peptides, 19 chains. Longest chain 271 peptides. Score 0.691 Round 2: 1670 peptides, 23 chains. Longest chain 280 peptides. Score 0.686 Round 3: 1664 peptides, 28 chains. Longest chain 177 peptides. Score 0.679 Round 4: 1664 peptides, 29 chains. Longest chain 195 peptides. Score 0.678 Round 5: 1660 peptides, 29 chains. Longest chain 157 peptides. Score 0.678 Taking the results from Round 1 Chains 19, Residues 1653, Estimated correctness of the model 88.8 % 14 chains (1625 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13930 restraints for refining 18598 atoms. Observations/parameters ratio is 3.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2270 (Rfree = 0.000) for 18598 atoms. Found 484 (484 requested) and removed 100 (242 requested) atoms. Cycle 27: After refmac, R = 0.2188 (Rfree = 0.000) for 18982 atoms. Found 432 (494 requested) and removed 96 (247 requested) atoms. Cycle 28: After refmac, R = 0.2140 (Rfree = 0.000) for 19318 atoms. Found 337 (503 requested) and removed 133 (251 requested) atoms. Cycle 29: After refmac, R = 0.2113 (Rfree = 0.000) for 19522 atoms. Found 285 (509 requested) and removed 175 (254 requested) atoms. Cycle 30: After refmac, R = 0.2095 (Rfree = 0.000) for 19632 atoms. Found 286 (511 requested) and removed 283 (255 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.23 1.35 NCS extension: 19 residues added (506 deleted due to clashes), 19655 seeds are put forward Round 1: 1682 peptides, 21 chains. Longest chain 282 peptides. Score 0.691 Round 2: 1679 peptides, 21 chains. Longest chain 277 peptides. Score 0.690 Round 3: 1676 peptides, 29 chains. Longest chain 280 peptides. Score 0.681 Round 4: 1656 peptides, 35 chains. Longest chain 187 peptides. Score 0.670 Round 5: 1650 peptides, 31 chains. Longest chain 216 peptides. Score 0.673 Taking the results from Round 1 Chains 22, Residues 1661, Estimated correctness of the model 88.8 % 15 chains (1632 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13985 restraints for refining 18287 atoms. Observations/parameters ratio is 3.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2244 (Rfree = 0.000) for 18287 atoms. Found 476 (476 requested) and removed 75 (238 requested) atoms. Cycle 32: After refmac, R = 0.2166 (Rfree = 0.000) for 18688 atoms. Found 487 (487 requested) and removed 59 (243 requested) atoms. Cycle 33: After refmac, R = 0.2123 (Rfree = 0.000) for 19116 atoms. Found 349 (498 requested) and removed 134 (249 requested) atoms. Cycle 34: After refmac, R = 0.2099 (Rfree = 0.000) for 19331 atoms. Found 305 (504 requested) and removed 137 (252 requested) atoms. Cycle 35: After refmac, R = 0.2083 (Rfree = 0.000) for 19499 atoms. Found 272 (508 requested) and removed 172 (254 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.23 1.35 NCS extension: 14 residues added (696 deleted due to clashes), 19616 seeds are put forward Round 1: 1673 peptides, 19 chains. Longest chain 280 peptides. Score 0.691 Round 2: 1677 peptides, 17 chains. Longest chain 281 peptides. Score 0.694 Round 3: 1663 peptides, 25 chains. Longest chain 254 peptides. Score 0.683 Round 4: 1660 peptides, 33 chains. Longest chain 129 peptides. Score 0.673 Round 5: 1668 peptides, 32 chains. Longest chain 198 peptides. Score 0.676 Taking the results from Round 2 Chains 17, Residues 1660, Estimated correctness of the model 89.0 % 13 chains (1631 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 14011 restraints for refining 18602 atoms. Observations/parameters ratio is 3.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2300 (Rfree = 0.000) for 18602 atoms. Found 485 (485 requested) and removed 62 (242 requested) atoms. Cycle 37: After refmac, R = 0.2177 (Rfree = 0.000) for 19025 atoms. Found 496 (496 requested) and removed 99 (248 requested) atoms. Cycle 38: After refmac, R = 0.2125 (Rfree = 0.000) for 19422 atoms. Found 354 (506 requested) and removed 176 (253 requested) atoms. Cycle 39: After refmac, R = 0.2098 (Rfree = 0.000) for 19600 atoms. Found 309 (511 requested) and removed 187 (255 requested) atoms. Cycle 40: After refmac, R = 0.2080 (Rfree = 0.000) for 19722 atoms. Found 304 (514 requested) and removed 204 (257 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.23 1.35 NCS extension: 36 residues added (682 deleted due to clashes), 19859 seeds are put forward Round 1: 1674 peptides, 22 chains. Longest chain 282 peptides. Score 0.688 Round 2: 1663 peptides, 20 chains. Longest chain 281 peptides. Score 0.688 Round 3: 1663 peptides, 23 chains. Longest chain 277 peptides. Score 0.685 Round 4: 1646 peptides, 36 chains. Longest chain 125 peptides. Score 0.667 Round 5: 1655 peptides, 38 chains. Longest chain 170 peptides. Score 0.666 Taking the results from Round 2 Chains 21, Residues 1643, Estimated correctness of the model 88.6 % 17 chains (1617 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13891 restraints for refining 18760 atoms. Observations/parameters ratio is 3.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2223 (Rfree = 0.000) for 18760 atoms. Found 489 (489 requested) and removed 73 (244 requested) atoms. Cycle 42: After refmac, R = 0.2149 (Rfree = 0.000) for 19176 atoms. Found 440 (500 requested) and removed 120 (250 requested) atoms. Cycle 43: After refmac, R = 0.2107 (Rfree = 0.000) for 19496 atoms. Found 353 (508 requested) and removed 159 (254 requested) atoms. Cycle 44: After refmac, R = 0.2089 (Rfree = 0.000) for 19690 atoms. Found 312 (513 requested) and removed 205 (256 requested) atoms. Cycle 45: After refmac, R = 0.2068 (Rfree = 0.000) for 19797 atoms. Found 326 (516 requested) and removed 194 (258 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.23 1.35 NCS extension: 45 residues added (1444 deleted due to clashes), 19974 seeds are put forward Round 1: 1663 peptides, 19 chains. Longest chain 188 peptides. Score 0.689 Round 2: 1666 peptides, 17 chains. Longest chain 281 peptides. Score 0.692 Round 3: 1639 peptides, 29 chains. Longest chain 204 peptides. Score 0.674 Round 4: 1654 peptides, 24 chains. Longest chain 246 peptides. Score 0.682 Round 5: 1647 peptides, 34 chains. Longest chain 220 peptides. Score 0.669 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 1649, Estimated correctness of the model 88.8 % 16 chains (1635 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 58 A and 61 A Built loop between residues 81 A and 84 A Built loop between residues 147 A and 150 A Built loop between residues 216 A and 219 A Built loop between residues 246 A and 254 A Built loop between residues 146 C and 150 C Built loop between residues 197 C and 200 C Built loop between residues 102 B and 106 B Built loop between residues 149 F and 154 F Built loop between residues 250 F and 254 F 8 chains (1673 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 14221 restraints for refining 13847 atoms. Observations/parameters ratio is 4.91 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2691 (Rfree = 0.000) for 13847 atoms. Found 340 (361 requested) and removed 0 (361 requested) atoms. Cycle 47: After refmac, R = 0.2546 (Rfree = 0.000) for 13847 atoms. Found 156 (369 requested) and removed 4 (184 requested) atoms. Cycle 48: After refmac, R = 0.2467 (Rfree = 0.000) for 13847 atoms. Found 86 (373 requested) and removed 6 (186 requested) atoms. Cycle 49: After refmac, R = 0.2423 (Rfree = 0.000) for 13847 atoms. Found 45 (375 requested) and removed 18 (187 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 05:31:58 GMT 2018 Job finished. TimeTaking 327.53 Used memory is bytes: 13637464