null Sun 23 Dec 22:23:10 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 2ii1-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-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/2ii1-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-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 ============================================================ Sun 23 Dec 22:23:19 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/2ii1-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-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 727 and 0 Target number of residues in the AU: 727 Target solvent content: 0.6456 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: 2ii1-4.0-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: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-4.0-parrot-hancs.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 4.000 Wilson plot Bfac: 75.38 8241 reflections ( 91.02 % complete ) and 0 restraints for refining 10645 atoms. Observations/parameters ratio is 0.19 ------------------------------------------------------ Starting model: R = 0.3334 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3141 (Rfree = 0.000) for 10645 atoms. Found 50 (50 requested) and removed 247 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 4.04 Search for helices and strands: 0 residues in 0 chains, 10524 seeds are put forward NCS extension: 0 residues added, 10524 seeds are put forward Round 1: 202 peptides, 45 chains. Longest chain 9 peptides. Score 0.213 Round 2: 235 peptides, 49 chains. Longest chain 10 peptides. Score 0.245 Round 3: 251 peptides, 50 chains. Longest chain 8 peptides. Score 0.266 Round 4: 264 peptides, 52 chains. Longest chain 10 peptides. Score 0.274 Round 5: 294 peptides, 57 chains. Longest chain 10 peptides. Score 0.289 Taking the results from Round 5 Chains 57, Residues 237, Estimated correctness of the model 0.0 % 6 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 22019 restraints for refining 8695 atoms. 21086 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2435 (Rfree = 0.000) for 8695 atoms. Found 34 (41 requested) and removed 81 (20 requested) atoms. Cycle 2: After refmac, R = 0.2363 (Rfree = 0.000) for 8567 atoms. Found 41 (41 requested) and removed 65 (20 requested) atoms. Cycle 3: After refmac, R = 0.2339 (Rfree = 0.000) for 8506 atoms. Found 40 (40 requested) and removed 51 (20 requested) atoms. Cycle 4: After refmac, R = 0.2163 (Rfree = 0.000) for 8441 atoms. Found 40 (40 requested) and removed 57 (20 requested) atoms. Cycle 5: After refmac, R = 0.1567 (Rfree = 0.000) for 8402 atoms. Found 16 (40 requested) and removed 34 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 8536 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 8542 seeds are put forward Round 1: 260 peptides, 58 chains. Longest chain 7 peptides. Score 0.221 Round 2: 280 peptides, 54 chains. Longest chain 11 peptides. Score 0.287 Round 3: 311 peptides, 62 chains. Longest chain 9 peptides. Score 0.281 Round 4: 310 peptides, 61 chains. Longest chain 11 peptides. Score 0.287 Round 5: 314 peptides, 60 chains. Longest chain 10 peptides. Score 0.301 Taking the results from Round 5 Chains 60, Residues 254, Estimated correctness of the model 0.0 % 9 chains (41 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 19928 restraints for refining 8115 atoms. 18884 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2095 (Rfree = 0.000) for 8115 atoms. Found 38 (38 requested) and removed 73 (19 requested) atoms. Cycle 7: After refmac, R = 0.1994 (Rfree = 0.000) for 8041 atoms. Found 38 (38 requested) and removed 75 (19 requested) atoms. Cycle 8: After refmac, R = 0.1949 (Rfree = 0.000) for 7978 atoms. Found 38 (38 requested) and removed 52 (19 requested) atoms. Cycle 9: After refmac, R = 0.1887 (Rfree = 0.000) for 7940 atoms. Found 37 (37 requested) and removed 50 (18 requested) atoms. Cycle 10: After refmac, R = 0.1769 (Rfree = 0.000) for 7904 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 3.95 Search for helices and strands: 0 residues in 0 chains, 8079 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8091 seeds are put forward Round 1: 344 peptides, 75 chains. Longest chain 7 peptides. Score 0.245 Round 2: 373 peptides, 68 chains. Longest chain 11 peptides. Score 0.341 Round 3: 372 peptides, 68 chains. Longest chain 13 peptides. Score 0.339 Round 4: 388 peptides, 72 chains. Longest chain 11 peptides. Score 0.337 Round 5: 413 peptides, 73 chains. Longest chain 13 peptides. Score 0.369 Taking the results from Round 5 Chains 73, Residues 340, Estimated correctness of the model 0.0 % 10 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 19477 restraints for refining 8235 atoms. 18063 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1904 (Rfree = 0.000) for 8235 atoms. Found 36 (39 requested) and removed 59 (19 requested) atoms. Cycle 12: After refmac, R = 0.1785 (Rfree = 0.000) for 8154 atoms. Found 39 (39 requested) and removed 52 (19 requested) atoms. Cycle 13: After refmac, R = 0.1755 (Rfree = 0.000) for 8106 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 14: After refmac, R = 0.1308 (Rfree = 0.000) for 8086 atoms. Found 14 (38 requested) and removed 28 (19 requested) atoms. Cycle 15: After refmac, R = 0.1244 (Rfree = 0.000) for 8060 atoms. Found 8 (38 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 4.03 Search for helices and strands: 0 residues in 0 chains, 8216 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 8233 seeds are put forward Round 1: 351 peptides, 78 chains. Longest chain 13 peptides. Score 0.235 Round 2: 385 peptides, 77 chains. Longest chain 9 peptides. Score 0.299 Round 3: 375 peptides, 70 chains. Longest chain 18 peptides. Score 0.330 Round 4: 378 peptides, 74 chains. Longest chain 9 peptides. Score 0.308 Round 5: 351 peptides, 66 chains. Longest chain 9 peptides. Score 0.319 Taking the results from Round 3 Chains 70, Residues 305, Estimated correctness of the model 0.0 % 9 chains (37 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 19607 restraints for refining 8229 atoms. 18373 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1769 (Rfree = 0.000) for 8229 atoms. Found 38 (39 requested) and removed 62 (19 requested) atoms. Cycle 17: After refmac, R = 0.1731 (Rfree = 0.000) for 8174 atoms. Found 38 (38 requested) and removed 55 (19 requested) atoms. Cycle 18: After refmac, R = 0.1670 (Rfree = 0.000) for 8142 atoms. Found 38 (38 requested) and removed 48 (19 requested) atoms. Cycle 19: After refmac, R = 0.1585 (Rfree = 0.000) for 8124 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 20: After refmac, R = 0.1195 (Rfree = 0.000) for 8120 atoms. Found 7 (38 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 8264 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 8281 seeds are put forward Round 1: 329 peptides, 73 chains. Longest chain 8 peptides. Score 0.233 Round 2: 358 peptides, 68 chains. Longest chain 14 peptides. Score 0.317 Round 3: 360 peptides, 68 chains. Longest chain 12 peptides. Score 0.320 Round 4: 373 peptides, 66 chains. Longest chain 16 peptides. Score 0.354 Round 5: 395 peptides, 71 chains. Longest chain 12 peptides. Score 0.355 Taking the results from Round 5 Chains 71, Residues 324, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 20521 restraints for refining 8487 atoms. 19202 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1807 (Rfree = 0.000) for 8487 atoms. Found 40 (40 requested) and removed 74 (20 requested) atoms. Cycle 22: After refmac, R = 0.1749 (Rfree = 0.000) for 8412 atoms. Found 40 (40 requested) and removed 64 (20 requested) atoms. Cycle 23: After refmac, R = 0.1716 (Rfree = 0.000) for 8361 atoms. Found 39 (39 requested) and removed 51 (19 requested) atoms. Cycle 24: After refmac, R = 0.1171 (Rfree = 0.000) for 8335 atoms. Found 13 (39 requested) and removed 27 (19 requested) atoms. Cycle 25: After refmac, R = 0.1042 (Rfree = 0.000) for 8305 atoms. Found 8 (39 requested) and removed 26 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 4.04 Search for helices and strands: 0 residues in 0 chains, 8463 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8475 seeds are put forward Round 1: 305 peptides, 69 chains. Longest chain 9 peptides. Score 0.220 Round 2: 336 peptides, 66 chains. Longest chain 12 peptides. Score 0.295 Round 3: 340 peptides, 62 chains. Longest chain 17 peptides. Score 0.329 Round 4: 336 peptides, 60 chains. Longest chain 12 peptides. Score 0.337 Round 5: 322 peptides, 57 chains. Longest chain 12 peptides. Score 0.335 Taking the results from Round 4 Chains 60, Residues 276, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 21166 restraints for refining 8577 atoms. 20097 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1696 (Rfree = 0.000) for 8577 atoms. Found 40 (40 requested) and removed 69 (20 requested) atoms. Cycle 27: After refmac, R = 0.1685 (Rfree = 0.000) for 8511 atoms. Found 40 (40 requested) and removed 47 (20 requested) atoms. Cycle 28: After refmac, R = 0.1552 (Rfree = 0.000) for 8485 atoms. Found 40 (40 requested) and removed 44 (20 requested) atoms. Cycle 29: After refmac, R = 0.1052 (Rfree = 0.000) for 8455 atoms. Found 20 (40 requested) and removed 34 (20 requested) atoms. Cycle 30: After refmac, R = 0.0936 (Rfree = 0.000) for 8429 atoms. Found 12 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 8602 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8617 seeds are put forward Round 1: 276 peptides, 60 chains. Longest chain 8 peptides. Score 0.235 Round 2: 302 peptides, 60 chains. Longest chain 10 peptides. Score 0.281 Round 3: 301 peptides, 59 chains. Longest chain 11 peptides. Score 0.286 Round 4: 306 peptides, 61 chains. Longest chain 11 peptides. Score 0.280 Round 5: 318 peptides, 62 chains. Longest chain 9 peptides. Score 0.293 Taking the results from Round 5 Chains 62, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 21268 restraints for refining 8505 atoms. 20306 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1695 (Rfree = 0.000) for 8505 atoms. Found 40 (40 requested) and removed 52 (20 requested) atoms. Cycle 32: After refmac, R = 0.1734 (Rfree = 0.000) for 8467 atoms. Found 40 (40 requested) and removed 50 (20 requested) atoms. Cycle 33: After refmac, R = 0.1674 (Rfree = 0.000) for 8440 atoms. Found 40 (40 requested) and removed 46 (20 requested) atoms. Cycle 34: After refmac, R = 0.1581 (Rfree = 0.000) for 8424 atoms. Found 40 (40 requested) and removed 39 (20 requested) atoms. Cycle 35: After refmac, R = 0.1441 (Rfree = 0.000) for 8402 atoms. Found 40 (40 requested) and removed 31 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 4.02 Search for helices and strands: 0 residues in 0 chains, 8566 seeds are put forward NCS extension: 0 residues added, 8566 seeds are put forward Round 1: 255 peptides, 60 chains. Longest chain 7 peptides. Score 0.196 Round 2: 282 peptides, 56 chains. Longest chain 9 peptides. Score 0.275 Round 3: 303 peptides, 61 chains. Longest chain 11 peptides. Score 0.275 Round 4: 301 peptides, 59 chains. Longest chain 10 peptides. Score 0.286 Round 5: 288 peptides, 53 chains. Longest chain 10 peptides. Score 0.308 Taking the results from Round 5 Chains 53, Residues 235, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 21266 restraints for refining 8498 atoms. 20379 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1628 (Rfree = 0.000) for 8498 atoms. Found 40 (40 requested) and removed 69 (20 requested) atoms. Cycle 37: After refmac, R = 0.1795 (Rfree = 0.000) for 8446 atoms. Found 40 (40 requested) and removed 58 (20 requested) atoms. Cycle 38: After refmac, R = 0.1592 (Rfree = 0.000) for 8419 atoms. Found 40 (40 requested) and removed 41 (20 requested) atoms. Cycle 39: After refmac, R = 0.1506 (Rfree = 0.000) for 8405 atoms. Found 39 (39 requested) and removed 39 (19 requested) atoms. Cycle 40: After refmac, R = 0.1538 (Rfree = 0.000) for 8390 atoms. Found 39 (39 requested) and removed 34 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 4.08 Search for helices and strands: 0 residues in 0 chains, 8574 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 8585 seeds are put forward Round 1: 265 peptides, 61 chains. Longest chain 9 peptides. Score 0.207 Round 2: 289 peptides, 59 chains. Longest chain 9 peptides. Score 0.265 Round 3: 281 peptides, 56 chains. Longest chain 9 peptides. Score 0.274 Round 4: 296 peptides, 56 chains. Longest chain 10 peptides. Score 0.300 Round 5: 294 peptides, 58 chains. Longest chain 11 peptides. Score 0.281 Taking the results from Round 4 Chains 56, Residues 240, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 21327 restraints for refining 8580 atoms. 20383 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1663 (Rfree = 0.000) for 8580 atoms. Found 40 (40 requested) and removed 52 (20 requested) atoms. Cycle 42: After refmac, R = 0.1557 (Rfree = 0.000) for 8528 atoms. Found 40 (40 requested) and removed 54 (20 requested) atoms. Cycle 43: After refmac, R = 0.1514 (Rfree = 0.000) for 8497 atoms. Found 40 (40 requested) and removed 44 (20 requested) atoms. Cycle 44: After refmac, R = 0.1408 (Rfree = 0.000) for 8479 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. Cycle 45: After refmac, R = 0.1379 (Rfree = 0.000) for 8476 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 4.04 Search for helices and strands: 0 residues in 0 chains, 8655 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 8664 seeds are put forward Round 1: 207 peptides, 48 chains. Longest chain 8 peptides. Score 0.198 Round 2: 221 peptides, 43 chains. Longest chain 8 peptides. Score 0.267 Round 3: 225 peptides, 45 chains. Longest chain 9 peptides. Score 0.258 Round 4: 245 peptides, 49 chains. Longest chain 10 peptides. Score 0.263 Round 5: 234 peptides, 44 chains. Longest chain 8 peptides. Score 0.283 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 190, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ii1-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8241 reflections ( 91.02 % complete ) and 21852 restraints for refining 8548 atoms. 21136 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1607 (Rfree = 0.000) for 8548 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.1720 (Rfree = 0.000) for 8508 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.1565 (Rfree = 0.000) for 8480 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.1833 (Rfree = 0.000) for 8445 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:59:47 GMT 2018 Job finished. TimeTaking 96.62 Used memory is bytes: 26115360