Mon 24 Dec 07:37:55 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 2ii1-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.8-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/2ii1-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.8-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 07:38:00 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/2ii1-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.8-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 748 and 0 Target number of residues in the AU: 748 Target solvent content: 0.6354 Checking the provided sequence file Detected sequence length: 301 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1204 Adjusted target solvent content: 0.41 Input MTZ file: 2ii1-3.8-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: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 9632 target number of atoms Had to go as low as 0.65 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 3 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: 91.283 3.800 Wilson plot Bfac: 69.22 9674 reflections ( 91.17 % complete ) and 0 restraints for refining 10682 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3337 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3019 (Rfree = 0.000) for 10682 atoms. Found 58 (58 requested) and removed 148 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 3.95 Search for helices and strands: 0 residues in 0 chains, 10702 seeds are put forward NCS extension: 0 residues added, 10702 seeds are put forward Round 1: 233 peptides, 53 chains. Longest chain 7 peptides. Score 0.209 Round 2: 289 peptides, 62 chains. Longest chain 11 peptides. Score 0.243 Round 3: 307 peptides, 65 chains. Longest chain 9 peptides. Score 0.253 Round 4: 333 peptides, 65 chains. Longest chain 11 peptides. Score 0.297 Round 5: 320 peptides, 61 chains. Longest chain 12 peptides. Score 0.304 Taking the results from Round 5 Chains 61, Residues 259, Estimated correctness of the model 0.0 % 6 chains (22 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21834 restraints for refining 8711 atoms. 20808 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2593 (Rfree = 0.000) for 8711 atoms. Found 47 (47 requested) and removed 49 (23 requested) atoms. Cycle 2: After refmac, R = 0.2407 (Rfree = 0.000) for 8609 atoms. Found 41 (47 requested) and removed 46 (23 requested) atoms. Cycle 3: After refmac, R = 0.2266 (Rfree = 0.000) for 8573 atoms. Found 47 (47 requested) and removed 48 (23 requested) atoms. Cycle 4: After refmac, R = 0.1756 (Rfree = 0.000) for 8533 atoms. Found 12 (47 requested) and removed 33 (23 requested) atoms. Cycle 5: After refmac, R = 0.1630 (Rfree = 0.000) for 8504 atoms. Found 12 (46 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.94 Search for helices and strands: 0 residues in 0 chains, 8658 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8673 seeds are put forward Round 1: 304 peptides, 70 chains. Longest chain 7 peptides. Score 0.211 Round 2: 399 peptides, 82 chains. Longest chain 9 peptides. Score 0.287 Round 3: 399 peptides, 77 chains. Longest chain 10 peptides. Score 0.321 Round 4: 414 peptides, 80 chains. Longest chain 11 peptides. Score 0.325 Round 5: 432 peptides, 82 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 5 Chains 82, Residues 350, Estimated correctness of the model 0.0 % 10 chains (39 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 19798 restraints for refining 8238 atoms. 18402 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1893 (Rfree = 0.000) for 8238 atoms. Found 28 (45 requested) and removed 54 (22 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.1852 (Rfree = 0.000) for 8172 atoms. Found 26 (45 requested) and removed 45 (22 requested) atoms. Cycle 8: After refmac, R = 0.1828 (Rfree = 0.000) for 8125 atoms. Found 40 (44 requested) and removed 45 (22 requested) atoms. Cycle 9: After refmac, R = 0.1407 (Rfree = 0.000) for 8096 atoms. Found 15 (44 requested) and removed 40 (22 requested) atoms. Cycle 10: After refmac, R = 0.1328 (Rfree = 0.000) for 8056 atoms. Found 14 (44 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.89 Search for helices and strands: 0 residues in 0 chains, 8224 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8236 seeds are put forward Round 1: 379 peptides, 80 chains. Longest chain 9 peptides. Score 0.268 Round 2: 423 peptides, 79 chains. Longest chain 17 peptides. Score 0.345 Round 3: 425 peptides, 81 chains. Longest chain 14 peptides. Score 0.335 Round 4: 418 peptides, 76 chains. Longest chain 13 peptides. Score 0.357 Round 5: 456 peptides, 79 chains. Longest chain 13 peptides. Score 0.394 Taking the results from Round 5 Chains 79, Residues 377, Estimated correctness of the model 0.0 % 8 chains (38 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 19934 restraints for refining 8456 atoms. 18397 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1997 (Rfree = 0.000) for 8456 atoms. Found 38 (46 requested) and removed 66 (23 requested) atoms. Cycle 12: After refmac, R = 0.1793 (Rfree = 0.000) for 8383 atoms. Found 35 (46 requested) and removed 52 (23 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1711 (Rfree = 0.000) for 8325 atoms. Found 35 (46 requested) and removed 34 (23 requested) atoms. Cycle 14: After refmac, R = 0.1613 (Rfree = 0.000) for 8296 atoms. Found 36 (45 requested) and removed 39 (22 requested) atoms. Cycle 15: After refmac, R = 0.1262 (Rfree = 0.000) for 8275 atoms. Found 12 (45 requested) and removed 29 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.86 Search for helices and strands: 0 residues in 0 chains, 8399 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 8415 seeds are put forward Round 1: 359 peptides, 77 chains. Longest chain 10 peptides. Score 0.256 Round 2: 399 peptides, 75 chains. Longest chain 12 peptides. Score 0.334 Round 3: 402 peptides, 71 chains. Longest chain 17 peptides. Score 0.365 Round 4: 394 peptides, 68 chains. Longest chain 15 peptides. Score 0.373 Round 5: 391 peptides, 70 chains. Longest chain 14 peptides. Score 0.355 Taking the results from Round 4 Chains 68, Residues 326, Estimated correctness of the model 0.0 % 6 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 20706 restraints for refining 8534 atoms. 19423 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1740 (Rfree = 0.000) for 8534 atoms. Found 44 (46 requested) and removed 76 (23 requested) atoms. Cycle 17: After refmac, R = 0.1662 (Rfree = 0.000) for 8473 atoms. Found 34 (46 requested) and removed 36 (23 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1678 (Rfree = 0.000) for 8449 atoms. Found 46 (46 requested) and removed 43 (23 requested) atoms. Cycle 19: After refmac, R = 0.1432 (Rfree = 0.000) for 8433 atoms. Found 26 (46 requested) and removed 41 (23 requested) atoms. Cycle 20: After refmac, R = 0.1676 (Rfree = 0.000) for 8401 atoms. Found 46 (46 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.92 Search for helices and strands: 0 residues in 0 chains, 8585 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 8608 seeds are put forward Round 1: 355 peptides, 76 chains. Longest chain 12 peptides. Score 0.256 Round 2: 407 peptides, 74 chains. Longest chain 13 peptides. Score 0.353 Round 3: 418 peptides, 71 chains. Longest chain 18 peptides. Score 0.389 Round 4: 418 peptides, 71 chains. Longest chain 18 peptides. Score 0.389 Round 5: 424 peptides, 71 chains. Longest chain 18 peptides. Score 0.398 Taking the results from Round 5 Chains 72, Residues 353, Estimated correctness of the model 0.0 % 9 chains (47 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 20401 restraints for refining 8576 atoms. 18950 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1670 (Rfree = 0.000) for 8576 atoms. Found 44 (47 requested) and removed 65 (23 requested) atoms. Cycle 22: After refmac, R = 0.1739 (Rfree = 0.000) for 8523 atoms. Found 43 (47 requested) and removed 62 (23 requested) atoms. Cycle 23: After refmac, R = 0.1753 (Rfree = 0.000) for 8481 atoms. Found 46 (46 requested) and removed 42 (23 requested) atoms. Cycle 24: After refmac, R = 0.1641 (Rfree = 0.000) for 8471 atoms. Found 46 (46 requested) and removed 37 (23 requested) atoms. Cycle 25: After refmac, R = 0.1265 (Rfree = 0.000) for 8468 atoms. Found 17 (46 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 8638 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8654 seeds are put forward Round 1: 349 peptides, 75 chains. Longest chain 8 peptides. Score 0.253 Round 2: 389 peptides, 76 chains. Longest chain 15 peptides. Score 0.312 Round 3: 384 peptides, 68 chains. Longest chain 15 peptides. Score 0.358 Round 4: 407 peptides, 70 chains. Longest chain 13 peptides. Score 0.379 Round 5: 401 peptides, 70 chains. Longest chain 13 peptides. Score 0.370 Taking the results from Round 4 Chains 70, Residues 337, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 20939 restraints for refining 8711 atoms. 19605 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1733 (Rfree = 0.000) for 8711 atoms. Found 45 (47 requested) and removed 67 (23 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1683 (Rfree = 0.000) for 8665 atoms. Found 47 (47 requested) and removed 49 (23 requested) atoms. Cycle 28: After refmac, R = 0.1622 (Rfree = 0.000) for 8650 atoms. Found 40 (47 requested) and removed 42 (23 requested) atoms. Cycle 29: After refmac, R = 0.1266 (Rfree = 0.000) for 8638 atoms. Found 9 (47 requested) and removed 28 (23 requested) atoms. Cycle 30: After refmac, R = 0.1217 (Rfree = 0.000) for 8613 atoms. Found 12 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.88 Search for helices and strands: 0 residues in 0 chains, 8762 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 8776 seeds are put forward Round 1: 322 peptides, 72 chains. Longest chain 8 peptides. Score 0.228 Round 2: 352 peptides, 69 chains. Longest chain 11 peptides. Score 0.300 Round 3: 371 peptides, 73 chains. Longest chain 12 peptides. Score 0.303 Round 4: 389 peptides, 75 chains. Longest chain 12 peptides. Score 0.319 Round 5: 381 peptides, 66 chains. Longest chain 16 peptides. Score 0.366 Taking the results from Round 5 Chains 66, Residues 315, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21326 restraints for refining 8712 atoms. 20088 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1595 (Rfree = 0.000) for 8712 atoms. Found 38 (47 requested) and removed 34 (23 requested) atoms. Cycle 32: After refmac, R = 0.1535 (Rfree = 0.000) for 8690 atoms. Found 40 (47 requested) and removed 39 (23 requested) atoms. Cycle 33: After refmac, R = 0.1199 (Rfree = 0.000) for 8675 atoms. Found 4 (47 requested) and removed 28 (23 requested) atoms. Cycle 34: After refmac, R = 0.1148 (Rfree = 0.000) for 8643 atoms. Found 5 (47 requested) and removed 26 (23 requested) atoms. Cycle 35: After refmac, R = 0.1165 (Rfree = 0.000) for 8615 atoms. Found 10 (47 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.89 Search for helices and strands: 0 residues in 0 chains, 8746 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8762 seeds are put forward Round 1: 322 peptides, 72 chains. Longest chain 9 peptides. Score 0.228 Round 2: 363 peptides, 69 chains. Longest chain 15 peptides. Score 0.318 Round 3: 362 peptides, 70 chains. Longest chain 13 peptides. Score 0.309 Round 4: 353 peptides, 60 chains. Longest chain 13 peptides. Score 0.364 Round 5: 352 peptides, 62 chains. Longest chain 19 peptides. Score 0.348 Taking the results from Round 4 Chains 62, Residues 293, Estimated correctness of the model 0.0 % 6 chains (33 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21327 restraints for refining 8712 atoms. 20131 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1487 (Rfree = 0.000) for 8712 atoms. Found 30 (47 requested) and removed 32 (23 requested) atoms. Cycle 37: After refmac, R = 0.1480 (Rfree = 0.000) for 8682 atoms. Found 31 (47 requested) and removed 29 (23 requested) atoms. Cycle 38: After refmac, R = 0.1451 (Rfree = 0.000) for 8670 atoms. Found 41 (47 requested) and removed 30 (23 requested) atoms. Cycle 39: After refmac, R = 0.1166 (Rfree = 0.000) for 8670 atoms. Found 10 (47 requested) and removed 24 (23 requested) atoms. Cycle 40: After refmac, R = 0.1182 (Rfree = 0.000) for 8652 atoms. Found 11 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.88 Search for helices and strands: 0 residues in 0 chains, 8797 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 8808 seeds are put forward Round 1: 309 peptides, 69 chains. Longest chain 10 peptides. Score 0.227 Round 2: 332 peptides, 68 chains. Longest chain 9 peptides. Score 0.274 Round 3: 330 peptides, 59 chains. Longest chain 13 peptides. Score 0.334 Round 4: 339 peptides, 64 chains. Longest chain 12 peptides. Score 0.314 Round 5: 320 peptides, 57 chains. Longest chain 12 peptides. Score 0.332 Taking the results from Round 3 Chains 59, Residues 271, Estimated correctness of the model 0.0 % 5 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21552 restraints for refining 8712 atoms. 20487 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1476 (Rfree = 0.000) for 8712 atoms. Found 42 (47 requested) and removed 30 (23 requested) atoms. Cycle 42: After refmac, R = 0.1501 (Rfree = 0.000) for 8716 atoms. Found 47 (47 requested) and removed 28 (23 requested) atoms. Cycle 43: After refmac, R = 0.1447 (Rfree = 0.000) for 8726 atoms. Found 41 (48 requested) and removed 33 (24 requested) atoms. Cycle 44: After refmac, R = 0.1473 (Rfree = 0.000) for 8723 atoms. Found 48 (48 requested) and removed 36 (24 requested) atoms. Cycle 45: After refmac, R = 0.1412 (Rfree = 0.000) for 8725 atoms. Found 39 (48 requested) and removed 34 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 8894 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8909 seeds are put forward Round 1: 270 peptides, 61 chains. Longest chain 8 peptides. Score 0.216 Round 2: 323 peptides, 64 chains. Longest chain 11 peptides. Score 0.287 Round 3: 321 peptides, 64 chains. Longest chain 17 peptides. Score 0.284 Round 4: 304 peptides, 55 chains. Longest chain 16 peptides. Score 0.320 Round 5: 290 peptides, 56 chains. Longest chain 16 peptides. Score 0.289 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 55, Residues 249, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2ii1-3_warpNtrace.pdb as input Building loops using Loopy2018 55 chains (249 residues) following loop building 4 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9674 reflections ( 91.17 % complete ) and 21710 restraints for refining 8712 atoms. 20731 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1568 (Rfree = 0.000) for 8712 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.1589 (Rfree = 0.000) for 8677 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.1477 (Rfree = 0.000) for 8644 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1039 (Rfree = 0.000) for 8614 atoms. TimeTaking 84.3