Tue 25 Dec 19:27:57 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 2aam-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aam-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aam-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-2.2-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/2aam-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-2.2-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 ============================================================ Tue 25 Dec 19:28:13 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/2aam-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-2.2-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 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-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: 4 Cell parameters: 195.000 84.610 194.910 90.000 119.891 90.000 Input sequence file: 2aam-2.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.35 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 16441 atoms. Observations/parameters ratio is 4.14 ------------------------------------------------------ Starting model: R = 0.3648 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3217 (Rfree = 0.000) for 16441 atoms. Found 428 (428 requested) and removed 225 (214 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.39 1.44 NCS extension: 0 residues added, 16644 seeds are put forward Round 1: 1514 peptides, 146 chains. Longest chain 43 peptides. Score 0.498 Round 2: 1526 peptides, 109 chains. Longest chain 60 peptides. Score 0.550 Round 3: 1573 peptides, 82 chains. Longest chain 71 peptides. Score 0.596 Round 4: 1586 peptides, 74 chains. Longest chain 92 peptides. Score 0.609 Round 5: 1581 peptides, 73 chains. Longest chain 78 peptides. Score 0.609 Taking the results from Round 5 Chains 92, Residues 1508, Estimated correctness of the model 82.7 % 41 chains (1257 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 272043 reflections ( 97.42 % complete ) and 11754 restraints for refining 17109 atoms. Observations/parameters ratio is 3.98 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3093 (Rfree = 0.000) for 17109 atoms. Found 446 (446 requested) and removed 231 (223 requested) atoms. Cycle 2: After refmac, R = 0.2847 (Rfree = 0.000) for 17324 atoms. Found 451 (451 requested) and removed 227 (225 requested) atoms. Cycle 3: After refmac, R = 0.2698 (Rfree = 0.000) for 17548 atoms. Found 457 (457 requested) and removed 162 (228 requested) atoms. Cycle 4: After refmac, R = 0.2640 (Rfree = 0.000) for 17843 atoms. Found 465 (465 requested) and removed 113 (232 requested) atoms. Cycle 5: After refmac, R = 0.2547 (Rfree = 0.000) for 18195 atoms. Found 428 (474 requested) and removed 137 (237 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.24 1.35 NCS extension: 300 residues added (793 deleted due to clashes), 18797 seeds are put forward Round 1: 1657 peptides, 45 chains. Longest chain 137 peptides. Score 0.659 Round 2: 1661 peptides, 38 chains. Longest chain 147 peptides. Score 0.667 Round 3: 1669 peptides, 38 chains. Longest chain 222 peptides. Score 0.669 Round 4: 1667 peptides, 31 chains. Longest chain 271 peptides. Score 0.677 Round 5: 1658 peptides, 45 chains. Longest chain 181 peptides. Score 0.659 Taking the results from Round 4 Chains 45, Residues 1636, Estimated correctness of the model 87.8 % 22 chains (1483 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 272043 reflections ( 97.42 % complete ) and 13230 restraints for refining 17521 atoms. Observations/parameters ratio is 3.88 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2735 (Rfree = 0.000) for 17521 atoms. Found 456 (456 requested) and removed 128 (228 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2601 (Rfree = 0.000) for 17849 atoms. Found 465 (465 requested) and removed 65 (232 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 8: After refmac, R = 0.2457 (Rfree = 0.000) for 18249 atoms. Found 474 (475 requested) and removed 95 (237 requested) atoms. Cycle 9: After refmac, R = 0.2374 (Rfree = 0.000) for 18628 atoms. Found 398 (485 requested) and removed 135 (242 requested) atoms. Cycle 10: After refmac, R = 0.2322 (Rfree = 0.000) for 18891 atoms. Found 324 (492 requested) and removed 152 (246 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.24 1.35 NCS extension: 254 residues added (2398 deleted due to clashes), 19319 seeds are put forward Round 1: 1667 peptides, 22 chains. Longest chain 182 peptides. Score 0.687 Round 2: 1671 peptides, 25 chains. Longest chain 199 peptides. Score 0.684 Round 3: 1659 peptides, 30 chains. Longest chain 148 peptides. Score 0.676 Round 4: 1657 peptides, 37 chains. Longest chain 129 peptides. Score 0.668 Round 5: 1671 peptides, 38 chains. Longest chain 163 peptides. Score 0.669 Taking the results from Round 1 Chains 25, Residues 1645, Estimated correctness of the model 88.5 % 19 chains (1584 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13720 restraints for refining 18025 atoms. Observations/parameters ratio is 3.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2502 (Rfree = 0.000) for 18025 atoms. Found 470 (470 requested) and removed 182 (235 requested) atoms. Cycle 12: After refmac, R = 0.2360 (Rfree = 0.000) for 18313 atoms. Found 477 (477 requested) and removed 108 (238 requested) atoms. Cycle 13: After refmac, R = 0.2279 (Rfree = 0.000) for 18682 atoms. Found 440 (487 requested) and removed 223 (243 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2244 (Rfree = 0.000) for 18899 atoms. Found 440 (492 requested) and removed 152 (246 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2198 (Rfree = 0.000) for 19187 atoms. Found 373 (500 requested) and removed 274 (250 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.23 1.35 NCS extension: 81 residues added (865 deleted due to clashes), 19368 seeds are put forward Round 1: 1676 peptides, 24 chains. Longest chain 269 peptides. Score 0.686 Round 2: 1688 peptides, 26 chains. Longest chain 174 peptides. Score 0.686 Round 3: 1676 peptides, 32 chains. Longest chain 273 peptides. Score 0.677 Round 4: 1678 peptides, 29 chains. Longest chain 280 peptides. Score 0.681 Round 5: 1641 peptides, 37 chains. Longest chain 133 peptides. Score 0.665 Taking the results from Round 2 Chains 27, Residues 1662, Estimated correctness of the model 88.4 % 20 chains (1639 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 14043 restraints for refining 18012 atoms. Observations/parameters ratio is 3.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2327 (Rfree = 0.000) for 18012 atoms. Found 469 (469 requested) and removed 80 (234 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2245 (Rfree = 0.000) for 18401 atoms. Found 479 (479 requested) and removed 80 (239 requested) atoms. Cycle 18: After refmac, R = 0.2201 (Rfree = 0.000) for 18800 atoms. Found 414 (490 requested) and removed 151 (245 requested) atoms. Cycle 19: After refmac, R = 0.2177 (Rfree = 0.000) for 19063 atoms. Found 382 (497 requested) and removed 202 (248 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2157 (Rfree = 0.000) for 19243 atoms. Found 359 (501 requested) and removed 204 (250 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.23 1.35 NCS extension: 8 residues added (669 deleted due to clashes), 19410 seeds are put forward Round 1: 1683 peptides, 21 chains. Longest chain 154 peptides. Score 0.691 Round 2: 1683 peptides, 21 chains. Longest chain 152 peptides. Score 0.691 Round 3: 1676 peptides, 22 chains. Longest chain 278 peptides. Score 0.688 Round 4: 1666 peptides, 30 chains. Longest chain 187 peptides. Score 0.678 Round 5: 1662 peptides, 29 chains. Longest chain 199 peptides. Score 0.678 Taking the results from Round 2 Chains 22, Residues 1662, Estimated correctness of the model 88.8 % 17 chains (1642 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 272043 reflections ( 97.42 % complete ) and 14036 restraints for refining 18366 atoms. Observations/parameters ratio is 3.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2282 (Rfree = 0.000) for 18366 atoms. Found 478 (478 requested) and removed 113 (239 requested) atoms. Cycle 22: After refmac, R = 0.2210 (Rfree = 0.000) for 18731 atoms. Found 458 (488 requested) and removed 116 (244 requested) atoms. Cycle 23: After refmac, R = 0.2162 (Rfree = 0.000) for 19073 atoms. Found 406 (497 requested) and removed 153 (248 requested) atoms. Cycle 24: After refmac, R = 0.2142 (Rfree = 0.000) for 19326 atoms. Found 340 (503 requested) and removed 199 (251 requested) atoms. Cycle 25: After refmac, R = 0.2121 (Rfree = 0.000) for 19467 atoms. Found 323 (507 requested) and removed 203 (253 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.23 1.35 NCS extension: 4 residues added (81 deleted due to clashes), 19594 seeds are put forward Round 1: 1681 peptides, 20 chains. Longest chain 212 peptides. Score 0.692 Round 2: 1683 peptides, 24 chains. Longest chain 215 peptides. Score 0.688 Round 3: 1667 peptides, 26 chains. Longest chain 152 peptides. Score 0.682 Round 4: 1651 peptides, 33 chains. Longest chain 175 peptides. Score 0.671 Round 5: 1652 peptides, 31 chains. Longest chain 144 peptides. Score 0.674 Taking the results from Round 1 Chains 20, Residues 1661, Estimated correctness of the model 88.8 % 15 chains (1634 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 14019 restraints for refining 18587 atoms. Observations/parameters ratio is 3.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2235 (Rfree = 0.000) for 18587 atoms. Found 484 (484 requested) and removed 71 (242 requested) atoms. Cycle 27: After refmac, R = 0.2170 (Rfree = 0.000) for 19000 atoms. Found 448 (495 requested) and removed 123 (247 requested) atoms. Cycle 28: After refmac, R = 0.2128 (Rfree = 0.000) for 19325 atoms. Found 358 (503 requested) and removed 172 (251 requested) atoms. Cycle 29: After refmac, R = 0.2109 (Rfree = 0.000) for 19511 atoms. Found 313 (508 requested) and removed 284 (254 requested) atoms. Cycle 30: After refmac, R = 0.2100 (Rfree = 0.000) for 19540 atoms. Found 393 (509 requested) and removed 202 (254 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.23 1.35 NCS extension: 68 residues added (612 deleted due to clashes), 19801 seeds are put forward Round 1: 1677 peptides, 26 chains. Longest chain 210 peptides. Score 0.684 Round 2: 1684 peptides, 24 chains. Longest chain 269 peptides. Score 0.688 Round 3: 1675 peptides, 26 chains. Longest chain 176 peptides. Score 0.684 Round 4: 1668 peptides, 27 chains. Longest chain 151 peptides. Score 0.681 Round 5: 1669 peptides, 28 chains. Longest chain 237 peptides. Score 0.680 Taking the results from Round 2 Chains 27, Residues 1660, Estimated correctness of the model 88.6 % 18 chains (1584 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 272043 reflections ( 97.42 % complete ) and 13737 restraints for refining 18691 atoms. Observations/parameters ratio is 3.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2236 (Rfree = 0.000) for 18691 atoms. Found 487 (487 requested) and removed 251 (243 requested) atoms. Cycle 32: After refmac, R = 0.2189 (Rfree = 0.000) for 18927 atoms. Found 493 (493 requested) and removed 165 (246 requested) atoms. Cycle 33: After refmac, R = 0.2143 (Rfree = 0.000) for 19255 atoms. Found 419 (502 requested) and removed 140 (251 requested) atoms. Cycle 34: After refmac, R = 0.2115 (Rfree = 0.000) for 19534 atoms. Found 297 (509 requested) and removed 209 (254 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2088 (Rfree = 0.000) for 19622 atoms. Found 331 (511 requested) and removed 287 (255 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.24 1.35 NCS extension: 89 residues added (1675 deleted due to clashes), 19756 seeds are put forward Round 1: 1677 peptides, 22 chains. Longest chain 210 peptides. Score 0.689 Round 2: 1678 peptides, 27 chains. Longest chain 161 peptides. Score 0.683 Round 3: 1680 peptides, 22 chains. Longest chain 148 peptides. Score 0.689 Round 4: 1641 peptides, 42 chains. Longest chain 140 peptides. Score 0.659 Round 5: 1660 peptides, 33 chains. Longest chain 152 peptides. Score 0.673 Taking the results from Round 3 Chains 26, Residues 1658, Estimated correctness of the model 88.6 % 19 chains (1621 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13888 restraints for refining 18493 atoms. Observations/parameters ratio is 3.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2244 (Rfree = 0.000) for 18493 atoms. Found 482 (482 requested) and removed 125 (241 requested) atoms. Cycle 37: After refmac, R = 0.2171 (Rfree = 0.000) for 18850 atoms. Found 491 (491 requested) and removed 57 (245 requested) atoms. Cycle 38: After refmac, R = 0.2129 (Rfree = 0.000) for 19284 atoms. Found 377 (502 requested) and removed 141 (251 requested) atoms. Cycle 39: After refmac, R = 0.2103 (Rfree = 0.000) for 19520 atoms. Found 307 (508 requested) and removed 172 (254 requested) atoms. Cycle 40: After refmac, R = 0.2087 (Rfree = 0.000) for 19655 atoms. Found 308 (512 requested) and removed 192 (256 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.24 1.35 NCS extension: 45 residues added (863 deleted due to clashes), 19818 seeds are put forward Round 1: 1681 peptides, 24 chains. Longest chain 269 peptides. Score 0.687 Round 2: 1664 peptides, 23 chains. Longest chain 181 peptides. Score 0.685 Round 3: 1670 peptides, 27 chains. Longest chain 282 peptides. Score 0.682 Round 4: 1670 peptides, 29 chains. Longest chain 270 peptides. Score 0.679 Round 5: 1658 peptides, 25 chains. Longest chain 203 peptides. Score 0.682 Taking the results from Round 1 Chains 26, Residues 1657, Estimated correctness of the model 88.5 % 20 chains (1546 residues) have been docked in sequence ------------------------------------------------------ 272043 reflections ( 97.42 % complete ) and 13617 restraints for refining 18766 atoms. Observations/parameters ratio is 3.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2273 (Rfree = 0.000) for 18766 atoms. Found 489 (489 requested) and removed 82 (244 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2167 (Rfree = 0.000) for 19173 atoms. Found 499 (499 requested) and removed 147 (249 requested) atoms. Cycle 43: After refmac, R = 0.2127 (Rfree = 0.000) for 19525 atoms. Found 382 (509 requested) and removed 280 (254 requested) atoms. Cycle 44: After refmac, R = 0.2118 (Rfree = 0.000) for 19627 atoms. Found 424 (511 requested) and removed 181 (255 requested) atoms. Cycle 45: After refmac, R = 0.2099 (Rfree = 0.000) for 19870 atoms. Found 320 (518 requested) and removed 216 (259 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.23 1.35 NCS extension: 26 residues added (676 deleted due to clashes), 20003 seeds are put forward Round 1: 1671 peptides, 29 chains. Longest chain 152 peptides. Score 0.680 Round 2: 1680 peptides, 22 chains. Longest chain 269 peptides. Score 0.689 Round 3: 1665 peptides, 34 chains. Longest chain 152 peptides. Score 0.673 Round 4: 1674 peptides, 26 chains. Longest chain 228 peptides. Score 0.684 Round 5: 1656 peptides, 32 chains. Longest chain 194 peptides. Score 0.673 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 1658, Estimated correctness of the model 88.6 % 16 chains (1551 residues) have been docked in sequence Sequence coverage is 93 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 57 C and 60 C Built loop between residues 133 B and 145 B Built loop between residues 214 B and 218 B Built loop between residues 143 E and 146 E Built loop between residues 168 E and 171 E Built loop between residues 143 D and 146 D Built loop between residues 189 D and 192 D Built loop between residues 73 F and 76 F Built loop between residues 142 F and 145 F Built loop between residues 250 F and 254 F 11 chains (1681 residues) following loop building 6 chains (1582 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 272043 reflections ( 97.42 % complete ) and 13814 restraints for refining 13455 atoms. Observations/parameters ratio is 5.05 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2772 (Rfree = 0.000) for 13455 atoms. Found 350 (350 requested) and removed 0 (350 requested) atoms. Cycle 47: After refmac, R = 0.2626 (Rfree = 0.000) for 13455 atoms. Found 222 (359 requested) and removed 3 (179 requested) atoms. Cycle 48: After refmac, R = 0.2534 (Rfree = 0.000) for 13455 atoms. Found 87 (365 requested) and removed 13 (182 requested) atoms. Cycle 49: After refmac, R = 0.2489 (Rfree = 0.000) for 13455 atoms. TimeTaking 352.4