null Mon 24 Dec 01:01:23 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 1vkd-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkd-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkd-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-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/1vkd-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-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 ============================================================ Mon 24 Dec 01:01:27 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/1vkd-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-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 1592 and 0 Target number of residues in the AU: 1592 Target solvent content: 0.6169 Checking the provided sequence file Detected sequence length: 338 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 2028 Adjusted target solvent content: 0.51 Input MTZ file: 1vkd-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: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 16224 target number of atoms Had to go as low as 0.70 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: 127.440 4.000 Wilson plot Bfac: 59.94 19706 reflections ( 99.63 % complete ) and 0 restraints for refining 18025 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3065 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2949 (Rfree = 0.000) for 18025 atoms. Found 85 (85 requested) and removed 86 (42 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 18222 seeds are put forward NCS extension: 0 residues added, 18222 seeds are put forward Round 1: 785 peptides, 156 chains. Longest chain 11 peptides. Score 0.303 Round 2: 1067 peptides, 169 chains. Longest chain 24 peptides. Score 0.466 Round 3: 1187 peptides, 174 chains. Longest chain 17 peptides. Score 0.527 Round 4: 1233 peptides, 175 chains. Longest chain 22 peptides. Score 0.552 Round 5: 1206 peptides, 162 chains. Longest chain 23 peptides. Score 0.569 Taking the results from Round 5 Chains 167, Residues 1044, Estimated correctness of the model 0.0 % 14 chains (103 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 32173 restraints for refining 14647 atoms. 27859 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2429 (Rfree = 0.000) for 14647 atoms. Found 49 (69 requested) and removed 97 (34 requested) atoms. Cycle 2: After refmac, R = 0.2242 (Rfree = 0.000) for 14357 atoms. Found 49 (69 requested) and removed 87 (34 requested) atoms. Cycle 3: After refmac, R = 0.2116 (Rfree = 0.000) for 14192 atoms. Found 54 (68 requested) and removed 79 (34 requested) atoms. Cycle 4: After refmac, R = 0.2045 (Rfree = 0.000) for 14080 atoms. Found 36 (67 requested) and removed 64 (33 requested) atoms. Cycle 5: After refmac, R = 0.2029 (Rfree = 0.000) for 13994 atoms. Found 49 (66 requested) and removed 63 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 14271 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 14294 seeds are put forward Round 1: 1004 peptides, 173 chains. Longest chain 17 peptides. Score 0.412 Round 2: 1149 peptides, 173 chains. Longest chain 21 peptides. Score 0.507 Round 3: 1136 peptides, 160 chains. Longest chain 21 peptides. Score 0.534 Round 4: 1166 peptides, 161 chains. Longest chain 18 peptides. Score 0.549 Round 5: 1198 peptides, 166 chains. Longest chain 23 peptides. Score 0.554 Taking the results from Round 5 Chains 168, Residues 1032, Estimated correctness of the model 0.0 % 11 chains (60 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33395 restraints for refining 14650 atoms. 29263 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2218 (Rfree = 0.000) for 14650 atoms. Found 54 (69 requested) and removed 89 (34 requested) atoms. Cycle 7: After refmac, R = 0.2131 (Rfree = 0.000) for 14464 atoms. Found 68 (69 requested) and removed 98 (34 requested) atoms. Cycle 8: After refmac, R = 0.1922 (Rfree = 0.000) for 14351 atoms. Found 52 (68 requested) and removed 78 (34 requested) atoms. Cycle 9: After refmac, R = 0.1862 (Rfree = 0.000) for 14266 atoms. Found 46 (68 requested) and removed 77 (34 requested) atoms. Cycle 10: After refmac, R = 0.1573 (Rfree = 0.000) for 14198 atoms. Found 13 (67 requested) and removed 52 (33 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 14472 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 14498 seeds are put forward Round 1: 1029 peptides, 190 chains. Longest chain 14 peptides. Score 0.378 Round 2: 1153 peptides, 168 chains. Longest chain 19 peptides. Score 0.523 Round 3: 1153 peptides, 163 chains. Longest chain 23 peptides. Score 0.536 Round 4: 1156 peptides, 160 chains. Longest chain 32 peptides. Score 0.546 Round 5: 1225 peptides, 171 chains. Longest chain 21 peptides. Score 0.557 Taking the results from Round 5 Chains 174, Residues 1054, Estimated correctness of the model 0.0 % 5 chains (59 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 32642 restraints for refining 14649 atoms. 28324 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2095 (Rfree = 0.000) for 14649 atoms. Found 58 (69 requested) and removed 91 (34 requested) atoms. Cycle 12: After refmac, R = 0.1922 (Rfree = 0.000) for 14480 atoms. Found 38 (69 requested) and removed 82 (34 requested) atoms. Cycle 13: After refmac, R = 0.1818 (Rfree = 0.000) for 14347 atoms. Found 30 (68 requested) and removed 73 (34 requested) atoms. Cycle 14: After refmac, R = 0.1604 (Rfree = 0.000) for 14252 atoms. Found 11 (67 requested) and removed 55 (33 requested) atoms. Cycle 15: After refmac, R = 0.1688 (Rfree = 0.000) for 14179 atoms. Found 21 (67 requested) and removed 62 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 14423 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 14439 seeds are put forward Round 1: 985 peptides, 181 chains. Longest chain 16 peptides. Score 0.374 Round 2: 1079 peptides, 170 chains. Longest chain 20 peptides. Score 0.471 Round 3: 1090 peptides, 163 chains. Longest chain 18 peptides. Score 0.498 Round 4: 1074 peptides, 156 chains. Longest chain 21 peptides. Score 0.507 Round 5: 1092 peptides, 156 chains. Longest chain 16 peptides. Score 0.518 Taking the results from Round 5 Chains 157, Residues 936, Estimated correctness of the model 0.0 % 9 chains (65 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33441 restraints for refining 14649 atoms. 29649 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2120 (Rfree = 0.000) for 14649 atoms. Found 61 (69 requested) and removed 86 (34 requested) atoms. Cycle 17: After refmac, R = 0.1937 (Rfree = 0.000) for 14484 atoms. Found 50 (69 requested) and removed 72 (34 requested) atoms. Cycle 18: After refmac, R = 0.1884 (Rfree = 0.000) for 14384 atoms. Found 49 (68 requested) and removed 66 (34 requested) atoms. Cycle 19: After refmac, R = 0.1570 (Rfree = 0.000) for 14323 atoms. Found 15 (68 requested) and removed 47 (34 requested) atoms. Cycle 20: After refmac, R = 0.1674 (Rfree = 0.000) for 14259 atoms. Found 29 (67 requested) and removed 50 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 14490 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 14506 seeds are put forward Round 1: 945 peptides, 181 chains. Longest chain 12 peptides. Score 0.344 Round 2: 1051 peptides, 161 chains. Longest chain 17 peptides. Score 0.478 Round 3: 1075 peptides, 163 chains. Longest chain 22 peptides. Score 0.488 Round 4: 1077 peptides, 164 chains. Longest chain 22 peptides. Score 0.487 Round 5: 1087 peptides, 161 chains. Longest chain 17 peptides. Score 0.501 Taking the results from Round 5 Chains 161, Residues 926, Estimated correctness of the model 0.0 % 7 chains (40 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33694 restraints for refining 14651 atoms. 30047 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1974 (Rfree = 0.000) for 14651 atoms. Found 49 (69 requested) and removed 83 (34 requested) atoms. Cycle 22: After refmac, R = 0.1850 (Rfree = 0.000) for 14504 atoms. Found 69 (69 requested) and removed 78 (34 requested) atoms. Cycle 23: After refmac, R = 0.1918 (Rfree = 0.000) for 14453 atoms. Found 68 (68 requested) and removed 68 (34 requested) atoms. Cycle 24: After refmac, R = 0.1780 (Rfree = 0.000) for 14376 atoms. Found 68 (68 requested) and removed 79 (34 requested) atoms. Cycle 25: After refmac, R = 0.1486 (Rfree = 0.000) for 14325 atoms. Found 29 (68 requested) and removed 50 (34 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 14607 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 14625 seeds are put forward Round 1: 883 peptides, 175 chains. Longest chain 15 peptides. Score 0.317 Round 2: 980 peptides, 165 chains. Longest chain 14 peptides. Score 0.419 Round 3: 1000 peptides, 154 chains. Longest chain 21 peptides. Score 0.465 Round 4: 1021 peptides, 156 chains. Longest chain 22 peptides. Score 0.473 Round 5: 1051 peptides, 149 chains. Longest chain 18 peptides. Score 0.512 Taking the results from Round 5 Chains 155, Residues 902, Estimated correctness of the model 0.0 % 8 chains (62 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33030 restraints for refining 14652 atoms. 29343 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2122 (Rfree = 0.000) for 14652 atoms. Found 64 (69 requested) and removed 115 (34 requested) atoms. Cycle 27: After refmac, R = 0.1871 (Rfree = 0.000) for 14513 atoms. Found 47 (69 requested) and removed 88 (34 requested) atoms. Cycle 28: After refmac, R = 0.1863 (Rfree = 0.000) for 14427 atoms. Found 68 (68 requested) and removed 74 (34 requested) atoms. Cycle 29: After refmac, R = 0.1919 (Rfree = 0.000) for 14386 atoms. Found 68 (68 requested) and removed 80 (34 requested) atoms. Cycle 30: After refmac, R = 0.1836 (Rfree = 0.000) for 14324 atoms. Found 68 (68 requested) and removed 60 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 14571 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 14586 seeds are put forward Round 1: 831 peptides, 159 chains. Longest chain 13 peptides. Score 0.329 Round 2: 910 peptides, 154 chains. Longest chain 16 peptides. Score 0.403 Round 3: 944 peptides, 155 chains. Longest chain 14 peptides. Score 0.424 Round 4: 958 peptides, 148 chains. Longest chain 18 peptides. Score 0.455 Round 5: 999 peptides, 152 chains. Longest chain 22 peptides. Score 0.470 Taking the results from Round 5 Chains 154, Residues 847, Estimated correctness of the model 0.0 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33665 restraints for refining 14652 atoms. 30261 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1976 (Rfree = 0.000) for 14652 atoms. Found 60 (69 requested) and removed 68 (34 requested) atoms. Cycle 32: After refmac, R = 0.1941 (Rfree = 0.000) for 14526 atoms. Found 69 (69 requested) and removed 66 (34 requested) atoms. Cycle 33: After refmac, R = 0.1889 (Rfree = 0.000) for 14478 atoms. Found 69 (69 requested) and removed 70 (34 requested) atoms. Cycle 34: After refmac, R = 0.1562 (Rfree = 0.000) for 14431 atoms. Found 26 (68 requested) and removed 51 (34 requested) atoms. Cycle 35: After refmac, R = 0.1745 (Rfree = 0.000) for 14369 atoms. Found 61 (68 requested) and removed 60 (34 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 14577 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 14596 seeds are put forward Round 1: 786 peptides, 156 chains. Longest chain 12 peptides. Score 0.303 Round 2: 892 peptides, 151 chains. Longest chain 23 peptides. Score 0.400 Round 3: 911 peptides, 149 chains. Longest chain 27 peptides. Score 0.419 Round 4: 922 peptides, 149 chains. Longest chain 16 peptides. Score 0.427 Round 5: 941 peptides, 145 chains. Longest chain 20 peptides. Score 0.452 Taking the results from Round 5 Chains 148, Residues 796, Estimated correctness of the model 0.0 % 9 chains (54 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33952 restraints for refining 14652 atoms. 30739 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1981 (Rfree = 0.000) for 14652 atoms. Found 69 (69 requested) and removed 85 (34 requested) atoms. Cycle 37: After refmac, R = 0.2039 (Rfree = 0.000) for 14550 atoms. Found 69 (69 requested) and removed 72 (34 requested) atoms. Cycle 38: After refmac, R = 0.1910 (Rfree = 0.000) for 14495 atoms. Found 69 (69 requested) and removed 63 (34 requested) atoms. Cycle 39: After refmac, R = 0.1869 (Rfree = 0.000) for 14443 atoms. Found 68 (68 requested) and removed 61 (34 requested) atoms. Cycle 40: After refmac, R = 0.1504 (Rfree = 0.000) for 14414 atoms. Found 24 (68 requested) and removed 45 (34 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 14606 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 14637 seeds are put forward Round 1: 757 peptides, 153 chains. Longest chain 12 peptides. Score 0.290 Round 2: 868 peptides, 152 chains. Longest chain 16 peptides. Score 0.379 Round 3: 900 peptides, 149 chains. Longest chain 18 peptides. Score 0.411 Round 4: 879 peptides, 148 chains. Longest chain 14 peptides. Score 0.400 Round 5: 911 peptides, 146 chains. Longest chain 14 peptides. Score 0.428 Taking the results from Round 5 Chains 147, Residues 765, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 34361 restraints for refining 14650 atoms. 31339 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2074 (Rfree = 0.000) for 14650 atoms. Found 69 (69 requested) and removed 85 (34 requested) atoms. Cycle 42: After refmac, R = 0.2067 (Rfree = 0.000) for 14545 atoms. Found 69 (69 requested) and removed 63 (34 requested) atoms. Cycle 43: After refmac, R = 0.1972 (Rfree = 0.000) for 14492 atoms. Found 69 (69 requested) and removed 70 (34 requested) atoms. Cycle 44: After refmac, R = 0.1935 (Rfree = 0.000) for 14432 atoms. Found 68 (68 requested) and removed 64 (34 requested) atoms. Cycle 45: After refmac, R = 0.1827 (Rfree = 0.000) for 14407 atoms. Found 68 (68 requested) and removed 65 (34 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 14646 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 14660 seeds are put forward Round 1: 629 peptides, 132 chains. Longest chain 10 peptides. Score 0.258 Round 2: 742 peptides, 137 chains. Longest chain 10 peptides. Score 0.333 Round 3: 751 peptides, 129 chains. Longest chain 19 peptides. Score 0.366 Round 4: 754 peptides, 129 chains. Longest chain 17 peptides. Score 0.368 Round 5: 783 peptides, 132 chains. Longest chain 15 peptides. Score 0.380 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 132, Residues 651, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vkd-4_warpNtrace.pdb as input Building loops using Loopy2018 132 chains (651 residues) following loop building 3 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19706 reflections ( 99.63 % complete ) and 35052 restraints for refining 14651 atoms. 32548 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1953 (Rfree = 0.000) for 14651 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.2040 (Rfree = 0.000) for 14559 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 48: After refmac, R = 0.1886 (Rfree = 0.000) for 14475 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 49: After refmac, R = 0.1516 (Rfree = 0.000) for 14411 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 03:19:07 GMT 2018 Job finished. TimeTaking 137.74 Used memory is bytes: 26479536