Sun 23 Dec 23:49:59 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 2ich-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ich-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ich-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-4.0-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/2ich-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-4.0-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 ============================================================ Sun 23 Dec 23:50:04 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/2ich-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-4.0-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 510 and 0 Target number of residues in the AU: 510 Target solvent content: 0.6251 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.51 Input MTZ file: 2ich-4.0-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: 19 Cell parameters: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.75 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: 29.160 4.000 Wilson plot Bfac: 63.72 6601 reflections ( 99.58 % complete ) and 0 restraints for refining 5912 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3160 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3097 (Rfree = 0.000) for 5912 atoms. Found 28 (28 requested) and removed 50 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 3.45 Search for helices and strands: 0 residues in 0 chains, 5978 seeds are put forward NCS extension: 0 residues added, 5978 seeds are put forward Round 1: 299 peptides, 58 chains. Longest chain 16 peptides. Score 0.333 Round 2: 373 peptides, 59 chains. Longest chain 13 peptides. Score 0.481 Round 3: 395 peptides, 55 chains. Longest chain 20 peptides. Score 0.554 Round 4: 409 peptides, 51 chains. Longest chain 22 peptides. Score 0.608 Round 5: 423 peptides, 54 chains. Longest chain 26 peptides. Score 0.608 Taking the results from Round 5 Chains 54, Residues 369, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 10464 restraints for refining 4839 atoms. 8922 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2469 (Rfree = 0.000) for 4839 atoms. Found 17 (23 requested) and removed 45 (11 requested) atoms. Cycle 2: After refmac, R = 0.2457 (Rfree = 0.000) for 4735 atoms. Found 15 (22 requested) and removed 53 (11 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2441 (Rfree = 0.000) for 4670 atoms. Found 18 (22 requested) and removed 36 (11 requested) atoms. Cycle 4: After refmac, R = 0.2136 (Rfree = 0.000) for 4637 atoms. Found 4 (22 requested) and removed 32 (11 requested) atoms. Cycle 5: After refmac, R = 0.2083 (Rfree = 0.000) for 4599 atoms. Found 6 (21 requested) and removed 30 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.43 Search for helices and strands: 0 residues in 0 chains, 4700 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4715 seeds are put forward Round 1: 337 peptides, 54 chains. Longest chain 24 peptides. Score 0.453 Round 2: 368 peptides, 53 chains. Longest chain 44 peptides. Score 0.522 Round 3: 379 peptides, 51 chains. Longest chain 26 peptides. Score 0.557 Round 4: 355 peptides, 48 chains. Longest chain 35 peptides. Score 0.539 Round 5: 375 peptides, 48 chains. Longest chain 26 peptides. Score 0.574 Taking the results from Round 5 Chains 48, Residues 327, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11127 restraints for refining 4841 atoms. 9798 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2504 (Rfree = 0.000) for 4841 atoms. Found 23 (23 requested) and removed 43 (11 requested) atoms. Cycle 7: After refmac, R = 0.2353 (Rfree = 0.000) for 4805 atoms. Found 22 (22 requested) and removed 43 (11 requested) atoms. Cycle 8: After refmac, R = 0.2142 (Rfree = 0.000) for 4770 atoms. Found 22 (22 requested) and removed 35 (11 requested) atoms. Cycle 9: After refmac, R = 0.1697 (Rfree = 0.000) for 4743 atoms. Found 4 (22 requested) and removed 27 (11 requested) atoms. Cycle 10: After refmac, R = 0.1782 (Rfree = 0.000) for 4712 atoms. Found 9 (22 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 4809 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4821 seeds are put forward Round 1: 312 peptides, 55 chains. Longest chain 18 peptides. Score 0.391 Round 2: 344 peptides, 50 chains. Longest chain 18 peptides. Score 0.501 Round 3: 347 peptides, 44 chains. Longest chain 20 peptides. Score 0.556 Round 4: 357 peptides, 49 chains. Longest chain 19 peptides. Score 0.534 Round 5: 364 peptides, 47 chains. Longest chain 19 peptides. Score 0.563 Taking the results from Round 5 Chains 49, Residues 317, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 10953 restraints for refining 4840 atoms. 9587 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2699 (Rfree = 0.000) for 4840 atoms. Found 23 (23 requested) and removed 46 (11 requested) atoms. Cycle 12: After refmac, R = 0.2217 (Rfree = 0.000) for 4786 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 13: After refmac, R = 0.2090 (Rfree = 0.000) for 4755 atoms. Found 22 (22 requested) and removed 43 (11 requested) atoms. Cycle 14: After refmac, R = 0.1950 (Rfree = 0.000) for 4715 atoms. Found 15 (22 requested) and removed 22 (11 requested) atoms. Cycle 15: After refmac, R = 0.1649 (Rfree = 0.000) for 4698 atoms. Found 6 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.46 Search for helices and strands: 0 residues in 0 chains, 4767 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4785 seeds are put forward Round 1: 319 peptides, 56 chains. Longest chain 12 peptides. Score 0.397 Round 2: 345 peptides, 53 chains. Longest chain 19 peptides. Score 0.478 Round 3: 359 peptides, 59 chains. Longest chain 14 peptides. Score 0.453 Round 4: 373 peptides, 56 chains. Longest chain 16 peptides. Score 0.506 Round 5: 353 peptides, 52 chains. Longest chain 15 peptides. Score 0.502 Taking the results from Round 4 Chains 56, Residues 317, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 10989 restraints for refining 4840 atoms. 9712 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2173 (Rfree = 0.000) for 4840 atoms. Found 19 (23 requested) and removed 37 (11 requested) atoms. Cycle 17: After refmac, R = 0.2084 (Rfree = 0.000) for 4802 atoms. Found 22 (22 requested) and removed 45 (11 requested) atoms. Cycle 18: After refmac, R = 0.1960 (Rfree = 0.000) for 4766 atoms. Found 15 (22 requested) and removed 40 (11 requested) atoms. Cycle 19: After refmac, R = 0.1908 (Rfree = 0.000) for 4731 atoms. Found 18 (22 requested) and removed 37 (11 requested) atoms. Cycle 20: After refmac, R = 0.1845 (Rfree = 0.000) for 4708 atoms. Found 13 (22 requested) and removed 35 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 4791 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4805 seeds are put forward Round 1: 309 peptides, 57 chains. Longest chain 10 peptides. Score 0.365 Round 2: 312 peptides, 47 chains. Longest chain 14 peptides. Score 0.464 Round 3: 324 peptides, 47 chains. Longest chain 20 peptides. Score 0.488 Round 4: 314 peptides, 49 chains. Longest chain 12 peptides. Score 0.450 Round 5: 323 peptides, 49 chains. Longest chain 21 peptides. Score 0.469 Taking the results from Round 3 Chains 47, Residues 277, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11332 restraints for refining 4841 atoms. 10237 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2055 (Rfree = 0.000) for 4841 atoms. Found 15 (23 requested) and removed 38 (11 requested) atoms. Cycle 22: After refmac, R = 0.1983 (Rfree = 0.000) for 4791 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Cycle 23: After refmac, R = 0.1916 (Rfree = 0.000) for 4766 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 24: After refmac, R = 0.1830 (Rfree = 0.000) for 4752 atoms. Found 18 (22 requested) and removed 25 (11 requested) atoms. Cycle 25: After refmac, R = 0.1813 (Rfree = 0.000) for 4740 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.45 Search for helices and strands: 0 residues in 0 chains, 4830 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4847 seeds are put forward Round 1: 284 peptides, 51 chains. Longest chain 14 peptides. Score 0.367 Round 2: 322 peptides, 51 chains. Longest chain 15 peptides. Score 0.449 Round 3: 319 peptides, 49 chains. Longest chain 15 peptides. Score 0.461 Round 4: 325 peptides, 46 chains. Longest chain 20 peptides. Score 0.499 Round 5: 320 peptides, 48 chains. Longest chain 14 peptides. Score 0.471 Taking the results from Round 4 Chains 46, Residues 279, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11173 restraints for refining 4841 atoms. 10070 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2122 (Rfree = 0.000) for 4841 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 27: After refmac, R = 0.1951 (Rfree = 0.000) for 4799 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 28: After refmac, R = 0.1907 (Rfree = 0.000) for 4780 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 29: After refmac, R = 0.1523 (Rfree = 0.000) for 4767 atoms. Found 10 (22 requested) and removed 23 (11 requested) atoms. Cycle 30: After refmac, R = 0.1617 (Rfree = 0.000) for 4747 atoms. Found 12 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.44 Search for helices and strands: 0 residues in 0 chains, 4842 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 4865 seeds are put forward Round 1: 271 peptides, 52 chains. Longest chain 12 peptides. Score 0.327 Round 2: 312 peptides, 48 chains. Longest chain 15 peptides. Score 0.455 Round 3: 312 peptides, 50 chains. Longest chain 20 peptides. Score 0.437 Round 4: 318 peptides, 46 chains. Longest chain 15 peptides. Score 0.485 Round 5: 344 peptides, 51 chains. Longest chain 15 peptides. Score 0.493 Taking the results from Round 5 Chains 51, Residues 293, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11301 restraints for refining 4841 atoms. 10163 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2520 (Rfree = 0.000) for 4841 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 32: After refmac, R = 0.2099 (Rfree = 0.000) for 4809 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 33: After refmac, R = 0.1861 (Rfree = 0.000) for 4785 atoms. Found 18 (22 requested) and removed 24 (11 requested) atoms. Cycle 34: After refmac, R = 0.1772 (Rfree = 0.000) for 4766 atoms. Found 21 (22 requested) and removed 29 (11 requested) atoms. Cycle 35: After refmac, R = 0.1711 (Rfree = 0.000) for 4753 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 4835 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 4859 seeds are put forward Round 1: 255 peptides, 51 chains. Longest chain 9 peptides. Score 0.299 Round 2: 290 peptides, 47 chains. Longest chain 19 peptides. Score 0.418 Round 3: 293 peptides, 49 chains. Longest chain 12 peptides. Score 0.406 Round 4: 302 peptides, 48 chains. Longest chain 14 peptides. Score 0.434 Round 5: 327 peptides, 51 chains. Longest chain 14 peptides. Score 0.459 Taking the results from Round 5 Chains 53, Residues 276, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11239 restraints for refining 4840 atoms. 10125 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2305 (Rfree = 0.000) for 4840 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 37: After refmac, R = 0.2113 (Rfree = 0.000) for 4817 atoms. Found 22 (22 requested) and removed 39 (11 requested) atoms. Cycle 38: After refmac, R = 0.1961 (Rfree = 0.000) for 4794 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 39: After refmac, R = 0.1904 (Rfree = 0.000) for 4782 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. Cycle 40: After refmac, R = 0.1516 (Rfree = 0.000) for 4764 atoms. Found 5 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.47 Search for helices and strands: 0 residues in 0 chains, 4851 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 4862 seeds are put forward Round 1: 264 peptides, 56 chains. Longest chain 9 peptides. Score 0.269 Round 2: 294 peptides, 50 chains. Longest chain 13 peptides. Score 0.399 Round 3: 295 peptides, 51 chains. Longest chain 16 peptides. Score 0.391 Round 4: 304 peptides, 49 chains. Longest chain 12 peptides. Score 0.429 Round 5: 306 peptides, 47 chains. Longest chain 17 peptides. Score 0.452 Taking the results from Round 5 Chains 48, Residues 259, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11227 restraints for refining 4841 atoms. 10168 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1982 (Rfree = 0.000) for 4841 atoms. Found 20 (23 requested) and removed 32 (11 requested) atoms. Cycle 42: After refmac, R = 0.1986 (Rfree = 0.000) for 4813 atoms. Found 22 (22 requested) and removed 35 (11 requested) atoms. Cycle 43: After refmac, R = 0.1928 (Rfree = 0.000) for 4788 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. Cycle 44: After refmac, R = 0.1836 (Rfree = 0.000) for 4770 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1732 (Rfree = 0.000) for 4753 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.44 Search for helices and strands: 0 residues in 0 chains, 4845 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4862 seeds are put forward Round 1: 242 peptides, 49 chains. Longest chain 10 peptides. Score 0.287 Round 2: 284 peptides, 53 chains. Longest chain 13 peptides. Score 0.347 Round 3: 287 peptides, 49 chains. Longest chain 20 peptides. Score 0.393 Round 4: 290 peptides, 48 chains. Longest chain 12 peptides. Score 0.409 Round 5: 296 peptides, 49 chains. Longest chain 11 peptides. Score 0.412 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 247, 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 2ich-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6601 reflections ( 99.58 % complete ) and 11458 restraints for refining 4841 atoms. 10519 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2035 (Rfree = 0.000) for 4841 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1977 (Rfree = 0.000) for 4819 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1893 (Rfree = 0.000) for 4798 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1786 (Rfree = 0.000) for 4776 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... TimeTaking 56.45