Mon 24 Dec 01:09:49 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 2awa-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2awa-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.6-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/2awa-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.6-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 01:09:53 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/2awa-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2awa-3.6-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 1162 and 0 Target number of residues in the AU: 1162 Target solvent content: 0.6530 Checking the provided sequence file Detected sequence length: 390 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1560 Adjusted target solvent content: 0.53 Input MTZ file: 2awa-3.6-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: 94.281 70.854 135.686 90.000 91.232 90.000 Input sequence file: 2awa-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12480 target number of atoms Had to go as low as 0.80 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: 135.654 3.600 Wilson plot Bfac: 80.06 20163 reflections ( 95.48 % complete ) and 0 restraints for refining 13866 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3519 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3079 (Rfree = 0.000) for 13866 atoms. Found 88 (88 requested) and removed 99 (44 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 14017 seeds are put forward NCS extension: 0 residues added, 14017 seeds are put forward Round 1: 552 peptides, 115 chains. Longest chain 11 peptides. Score 0.267 Round 2: 686 peptides, 128 chains. Longest chain 14 peptides. Score 0.345 Round 3: 753 peptides, 128 chains. Longest chain 13 peptides. Score 0.406 Round 4: 797 peptides, 127 chains. Longest chain 23 peptides. Score 0.447 Round 5: 801 peptides, 131 chains. Longest chain 14 peptides. Score 0.436 Taking the results from Round 4 Chains 129, Residues 670, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 25845 restraints for refining 11309 atoms. 23191 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2542 (Rfree = 0.000) for 11309 atoms. Found 48 (72 requested) and removed 71 (36 requested) atoms. Cycle 2: After refmac, R = 0.2406 (Rfree = 0.000) for 11116 atoms. Found 42 (72 requested) and removed 58 (36 requested) atoms. Cycle 3: After refmac, R = 0.2319 (Rfree = 0.000) for 11030 atoms. Found 47 (71 requested) and removed 57 (35 requested) atoms. Cycle 4: After refmac, R = 0.2206 (Rfree = 0.000) for 10963 atoms. Found 31 (70 requested) and removed 55 (35 requested) atoms. Cycle 5: After refmac, R = 0.2127 (Rfree = 0.000) for 10898 atoms. Found 36 (70 requested) and removed 52 (35 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.36 Search for helices and strands: 0 residues in 0 chains, 11201 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 11235 seeds are put forward Round 1: 671 peptides, 130 chains. Longest chain 12 peptides. Score 0.322 Round 2: 757 peptides, 129 chains. Longest chain 15 peptides. Score 0.405 Round 3: 806 peptides, 122 chains. Longest chain 18 peptides. Score 0.473 Round 4: 787 peptides, 126 chains. Longest chain 22 peptides. Score 0.442 Round 5: 812 peptides, 125 chains. Longest chain 18 peptides. Score 0.467 Taking the results from Round 3 Chains 122, Residues 684, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 25285 restraints for refining 11089 atoms. 22671 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2154 (Rfree = 0.000) for 11089 atoms. Found 37 (71 requested) and removed 57 (35 requested) atoms. Cycle 7: After refmac, R = 0.2034 (Rfree = 0.000) for 11001 atoms. Found 29 (71 requested) and removed 61 (35 requested) atoms. Cycle 8: After refmac, R = 0.1948 (Rfree = 0.000) for 10924 atoms. Found 24 (70 requested) and removed 52 (35 requested) atoms. Cycle 9: After refmac, R = 0.1889 (Rfree = 0.000) for 10862 atoms. Found 18 (69 requested) and removed 50 (34 requested) atoms. Cycle 10: After refmac, R = 0.1624 (Rfree = 0.000) for 10813 atoms. Found 10 (69 requested) and removed 40 (34 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.38 Search for helices and strands: 0 residues in 0 chains, 11079 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11096 seeds are put forward Round 1: 722 peptides, 132 chains. Longest chain 14 peptides. Score 0.362 Round 2: 752 peptides, 119 chains. Longest chain 15 peptides. Score 0.439 Round 3: 787 peptides, 124 chains. Longest chain 22 peptides. Score 0.450 Round 4: 779 peptides, 117 chains. Longest chain 19 peptides. Score 0.469 Round 5: 838 peptides, 121 chains. Longest chain 18 peptides. Score 0.502 Taking the results from Round 5 Chains 121, Residues 717, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20163 reflections ( 95.48 % complete ) and 25298 restraints for refining 11308 atoms. 22551 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2202 (Rfree = 0.000) for 11308 atoms. Found 53 (72 requested) and removed 63 (36 requested) atoms. Cycle 12: After refmac, R = 0.2040 (Rfree = 0.000) for 11223 atoms. Found 50 (72 requested) and removed 56 (36 requested) atoms. Cycle 13: After refmac, R = 0.1929 (Rfree = 0.000) for 11185 atoms. Found 23 (71 requested) and removed 49 (35 requested) atoms. Cycle 14: After refmac, R = 0.1860 (Rfree = 0.000) for 11135 atoms. Found 15 (71 requested) and removed 42 (35 requested) atoms. Cycle 15: After refmac, R = 0.1856 (Rfree = 0.000) for 11090 atoms. Found 23 (71 requested) and removed 50 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.38 Search for helices and strands: 0 residues in 0 chains, 11320 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 11336 seeds are put forward Round 1: 730 peptides, 142 chains. Longest chain 13 peptides. Score 0.330 Round 2: 785 peptides, 121 chains. Longest chain 15 peptides. Score 0.459 Round 3: 799 peptides, 126 chains. Longest chain 21 peptides. Score 0.452 Round 4: 814 peptides, 120 chains. Longest chain 23 peptides. Score 0.486 Round 5: 817 peptides, 126 chains. Longest chain 19 peptides. Score 0.467 Taking the results from Round 4 Chains 120, Residues 694, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 25321 restraints for refining 11312 atoms. 22636 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2110 (Rfree = 0.000) for 11312 atoms. Found 42 (72 requested) and removed 55 (36 requested) atoms. Cycle 17: After refmac, R = 0.2063 (Rfree = 0.000) for 11227 atoms. Found 39 (72 requested) and removed 53 (36 requested) atoms. Cycle 18: After refmac, R = 0.1980 (Rfree = 0.000) for 11174 atoms. Found 36 (71 requested) and removed 43 (35 requested) atoms. Cycle 19: After refmac, R = 0.1902 (Rfree = 0.000) for 11142 atoms. Found 35 (71 requested) and removed 43 (35 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1652 (Rfree = 0.000) for 11125 atoms. Found 7 (71 requested) and removed 42 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.39 Search for helices and strands: 0 residues in 0 chains, 11337 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 11354 seeds are put forward Round 1: 686 peptides, 131 chains. Longest chain 12 peptides. Score 0.333 Round 2: 743 peptides, 121 chains. Longest chain 17 peptides. Score 0.423 Round 3: 755 peptides, 118 chains. Longest chain 17 peptides. Score 0.445 Round 4: 742 peptides, 112 chains. Longest chain 19 peptides. Score 0.456 Round 5: 751 peptides, 110 chains. Longest chain 15 peptides. Score 0.471 Taking the results from Round 5 Chains 110, Residues 641, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20163 reflections ( 95.48 % complete ) and 26104 restraints for refining 11311 atoms. 23650 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1972 (Rfree = 0.000) for 11311 atoms. Found 41 (72 requested) and removed 47 (36 requested) atoms. Cycle 22: After refmac, R = 0.1875 (Rfree = 0.000) for 11245 atoms. Found 28 (72 requested) and removed 46 (36 requested) atoms. Cycle 23: After refmac, R = 0.1831 (Rfree = 0.000) for 11199 atoms. Found 27 (72 requested) and removed 42 (36 requested) atoms. Cycle 24: After refmac, R = 0.1780 (Rfree = 0.000) for 11170 atoms. Found 37 (71 requested) and removed 40 (35 requested) atoms. Cycle 25: After refmac, R = 0.1733 (Rfree = 0.000) for 11157 atoms. Found 24 (71 requested) and removed 41 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.38 Search for helices and strands: 0 residues in 0 chains, 11407 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11423 seeds are put forward Round 1: 634 peptides, 117 chains. Longest chain 14 peptides. Score 0.340 Round 2: 758 peptides, 121 chains. Longest chain 22 peptides. Score 0.436 Round 3: 731 peptides, 117 chains. Longest chain 17 peptides. Score 0.428 Round 4: 741 peptides, 110 chains. Longest chain 17 peptides. Score 0.463 Round 5: 739 peptides, 114 chains. Longest chain 25 peptides. Score 0.446 Taking the results from Round 4 Chains 110, Residues 631, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 25579 restraints for refining 11313 atoms. 23130 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1961 (Rfree = 0.000) for 11313 atoms. Found 40 (72 requested) and removed 43 (36 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1917 (Rfree = 0.000) for 11266 atoms. Found 43 (72 requested) and removed 54 (36 requested) atoms. Cycle 28: After refmac, R = 0.1843 (Rfree = 0.000) for 11240 atoms. Found 36 (72 requested) and removed 43 (36 requested) atoms. Cycle 29: After refmac, R = 0.1823 (Rfree = 0.000) for 11221 atoms. Found 42 (72 requested) and removed 45 (36 requested) atoms. Cycle 30: After refmac, R = 0.1784 (Rfree = 0.000) for 11214 atoms. Found 37 (71 requested) and removed 40 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.39 Search for helices and strands: 0 residues in 0 chains, 11408 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 11423 seeds are put forward Round 1: 638 peptides, 127 chains. Longest chain 13 peptides. Score 0.303 Round 2: 707 peptides, 122 chains. Longest chain 13 peptides. Score 0.388 Round 3: 743 peptides, 124 chains. Longest chain 16 peptides. Score 0.412 Round 4: 725 peptides, 114 chains. Longest chain 15 peptides. Score 0.434 Round 5: 728 peptides, 116 chains. Longest chain 16 peptides. Score 0.429 Taking the results from Round 4 Chains 114, Residues 611, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 25847 restraints for refining 11313 atoms. 23493 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1952 (Rfree = 0.000) for 11313 atoms. Found 35 (72 requested) and removed 41 (36 requested) atoms. Cycle 32: After refmac, R = 0.1928 (Rfree = 0.000) for 11251 atoms. Found 58 (72 requested) and removed 43 (36 requested) atoms. Cycle 33: After refmac, R = 0.1857 (Rfree = 0.000) for 11244 atoms. Found 43 (72 requested) and removed 44 (36 requested) atoms. Cycle 34: After refmac, R = 0.1776 (Rfree = 0.000) for 11231 atoms. Found 34 (72 requested) and removed 41 (36 requested) atoms. Cycle 35: After refmac, R = 0.1785 (Rfree = 0.000) for 11209 atoms. Found 46 (72 requested) and removed 44 (36 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.39 Search for helices and strands: 0 residues in 0 chains, 11474 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11490 seeds are put forward Round 1: 604 peptides, 129 chains. Longest chain 11 peptides. Score 0.260 Round 2: 683 peptides, 119 chains. Longest chain 16 peptides. Score 0.378 Round 3: 700 peptides, 121 chains. Longest chain 13 peptides. Score 0.385 Round 4: 689 peptides, 115 chains. Longest chain 13 peptides. Score 0.399 Round 5: 696 peptides, 116 chains. Longest chain 18 peptides. Score 0.401 Taking the results from Round 5 Chains 117, Residues 580, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 25951 restraints for refining 11313 atoms. 23708 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1935 (Rfree = 0.000) for 11313 atoms. Found 33 (72 requested) and removed 48 (36 requested) atoms. Cycle 37: After refmac, R = 0.1836 (Rfree = 0.000) for 11248 atoms. Found 44 (72 requested) and removed 39 (36 requested) atoms. Cycle 38: After refmac, R = 0.1825 (Rfree = 0.000) for 11237 atoms. Found 40 (72 requested) and removed 40 (36 requested) atoms. Cycle 39: After refmac, R = 0.1801 (Rfree = 0.000) for 11222 atoms. Found 54 (72 requested) and removed 40 (36 requested) atoms. Cycle 40: After refmac, R = 0.1780 (Rfree = 0.000) for 11222 atoms. Found 39 (72 requested) and removed 39 (36 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 11458 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 11474 seeds are put forward Round 1: 539 peptides, 112 chains. Longest chain 11 peptides. Score 0.266 Round 2: 616 peptides, 109 chains. Longest chain 14 peptides. Score 0.356 Round 3: 613 peptides, 105 chains. Longest chain 17 peptides. Score 0.369 Round 4: 623 peptides, 108 chains. Longest chain 16 peptides. Score 0.366 Round 5: 643 peptides, 105 chains. Longest chain 17 peptides. Score 0.397 Taking the results from Round 5 Chains 105, Residues 538, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 26430 restraints for refining 11313 atoms. 24383 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1868 (Rfree = 0.000) for 11313 atoms. Found 50 (72 requested) and removed 41 (36 requested) atoms. Cycle 42: After refmac, R = 0.1804 (Rfree = 0.000) for 11278 atoms. Found 28 (72 requested) and removed 40 (36 requested) atoms. Cycle 43: After refmac, R = 0.1777 (Rfree = 0.000) for 11241 atoms. Found 47 (72 requested) and removed 41 (36 requested) atoms. Cycle 44: After refmac, R = 0.1812 (Rfree = 0.000) for 11228 atoms. Found 53 (72 requested) and removed 42 (36 requested) atoms. Cycle 45: After refmac, R = 0.1742 (Rfree = 0.000) for 11223 atoms. Found 28 (72 requested) and removed 40 (36 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 11452 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 11473 seeds are put forward Round 1: 510 peptides, 110 chains. Longest chain 12 peptides. Score 0.245 Round 2: 615 peptides, 117 chains. Longest chain 17 peptides. Score 0.322 Round 3: 637 peptides, 112 chains. Longest chain 14 peptides. Score 0.363 Round 4: 627 peptides, 109 chains. Longest chain 14 peptides. Score 0.366 Round 5: 621 peptides, 102 chains. Longest chain 16 peptides. Score 0.389 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 102, Residues 519, 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 2awa-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20163 reflections ( 95.48 % complete ) and 26524 restraints for refining 11313 atoms. 24550 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1854 (Rfree = 0.000) for 11313 atoms. Found 0 (72 requested) and removed 36 (36 requested) atoms. Cycle 47: After refmac, R = 0.1841 (Rfree = 0.000) for 11237 atoms. Found 0 (72 requested) and removed 36 (36 requested) atoms. Cycle 48: After refmac, R = 0.1826 (Rfree = 0.000) for 11174 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.1825 (Rfree = 0.000) for 11121 atoms. TimeTaking 113.78