Mon 24 Dec 01:06:20 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 2hq7-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hq7-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hq7-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.4-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/2hq7-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.4-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 01:06:25 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/2hq7-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-3.4-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 194 and 0 Target number of residues in the AU: 194 Target solvent content: 0.6293 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-3.4-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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2336 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: 89.671 3.400 Wilson plot Bfac: 66.03 4012 reflections ( 99.41 % complete ) and 0 restraints for refining 2597 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3165 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2885 (Rfree = 0.000) for 2597 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.54 Search for helices and strands: 0 residues in 0 chains, 2641 seeds are put forward NCS extension: 0 residues added, 2641 seeds are put forward Round 1: 135 peptides, 25 chains. Longest chain 11 peptides. Score 0.383 Round 2: 187 peptides, 25 chains. Longest chain 17 peptides. Score 0.630 Round 3: 182 peptides, 20 chains. Longest chain 27 peptides. Score 0.694 Round 4: 194 peptides, 22 chains. Longest chain 23 peptides. Score 0.703 Round 5: 194 peptides, 23 chains. Longest chain 24 peptides. Score 0.688 Taking the results from Round 4 Chains 22, Residues 172, Estimated correctness of the model 58.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4607 restraints for refining 2124 atoms. 3941 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2088 (Rfree = 0.000) for 2124 atoms. Found 12 (16 requested) and removed 13 (8 requested) atoms. Cycle 2: After refmac, R = 0.1983 (Rfree = 0.000) for 2099 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. Cycle 3: After refmac, R = 0.1913 (Rfree = 0.000) for 2087 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.1824 (Rfree = 0.000) for 2076 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 5: After refmac, R = 0.1872 (Rfree = 0.000) for 2064 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.55 Search for helices and strands: 0 residues in 0 chains, 2150 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 2177 seeds are put forward Round 1: 158 peptides, 20 chains. Longest chain 21 peptides. Score 0.604 Round 2: 173 peptides, 21 chains. Longest chain 20 peptides. Score 0.645 Round 3: 177 peptides, 21 chains. Longest chain 14 peptides. Score 0.660 Round 4: 174 peptides, 20 chains. Longest chain 25 peptides. Score 0.666 Round 5: 179 peptides, 21 chains. Longest chain 15 peptides. Score 0.667 Taking the results from Round 5 Chains 21, Residues 158, Estimated correctness of the model 49.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4685 restraints for refining 2098 atoms. 4074 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1998 (Rfree = 0.000) for 2098 atoms. Found 8 (13 requested) and removed 11 (7 requested) atoms. Cycle 7: After refmac, R = 0.1923 (Rfree = 0.000) for 2084 atoms. Found 6 (13 requested) and removed 8 (7 requested) atoms. Cycle 8: After refmac, R = 0.1807 (Rfree = 0.000) for 2077 atoms. Found 3 (13 requested) and removed 7 (7 requested) atoms. Cycle 9: After refmac, R = 0.1876 (Rfree = 0.000) for 2071 atoms. Found 9 (13 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.2259 (Rfree = 0.000) for 2068 atoms. Found 13 (13 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.49 Search for helices and strands: 0 residues in 0 chains, 2157 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2171 seeds are put forward Round 1: 156 peptides, 23 chains. Longest chain 15 peptides. Score 0.536 Round 2: 175 peptides, 22 chains. Longest chain 18 peptides. Score 0.636 Round 3: 168 peptides, 20 chains. Longest chain 15 peptides. Score 0.644 Round 4: 177 peptides, 22 chains. Longest chain 23 peptides. Score 0.643 Round 5: 179 peptides, 21 chains. Longest chain 19 peptides. Score 0.667 Taking the results from Round 5 Chains 22, Residues 158, Estimated correctness of the model 49.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4743 restraints for refining 2124 atoms. 4075 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2021 (Rfree = 0.000) for 2124 atoms. Found 7 (14 requested) and removed 21 (8 requested) atoms. Cycle 12: After refmac, R = 0.1890 (Rfree = 0.000) for 2102 atoms. Found 5 (13 requested) and removed 9 (7 requested) atoms. Cycle 13: After refmac, R = 0.1800 (Rfree = 0.000) for 2094 atoms. Found 0 (13 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.1744 (Rfree = 0.000) for 2086 atoms. Found 3 (13 requested) and removed 7 (7 requested) atoms. Cycle 15: After refmac, R = 0.1704 (Rfree = 0.000) for 2081 atoms. Found 0 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.55 Search for helices and strands: 0 residues in 0 chains, 2149 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2167 seeds are put forward Round 1: 157 peptides, 25 chains. Longest chain 12 peptides. Score 0.499 Round 2: 172 peptides, 22 chains. Longest chain 22 peptides. Score 0.624 Round 3: 167 peptides, 23 chains. Longest chain 12 peptides. Score 0.585 Round 4: 168 peptides, 20 chains. Longest chain 20 peptides. Score 0.644 Round 5: 166 peptides, 24 chains. Longest chain 12 peptides. Score 0.562 Taking the results from Round 4 Chains 20, Residues 148, Estimated correctness of the model 42.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4967 restraints for refining 2124 atoms. 4395 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2016 (Rfree = 0.000) for 2124 atoms. Found 11 (14 requested) and removed 14 (8 requested) atoms. Cycle 17: After refmac, R = 0.1823 (Rfree = 0.000) for 2118 atoms. Found 9 (14 requested) and removed 8 (8 requested) atoms. Cycle 18: After refmac, R = 0.1754 (Rfree = 0.000) for 2118 atoms. Found 3 (13 requested) and removed 9 (7 requested) atoms. Cycle 19: After refmac, R = 0.1697 (Rfree = 0.000) for 2112 atoms. Found 5 (13 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.1652 (Rfree = 0.000) for 2108 atoms. Found 2 (13 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.53 Search for helices and strands: 0 residues in 0 chains, 2170 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 2199 seeds are put forward Round 1: 135 peptides, 18 chains. Longest chain 13 peptides. Score 0.541 Round 2: 157 peptides, 20 chains. Longest chain 22 peptides. Score 0.600 Round 3: 164 peptides, 20 chains. Longest chain 21 peptides. Score 0.628 Round 4: 160 peptides, 20 chains. Longest chain 22 peptides. Score 0.612 Round 5: 168 peptides, 20 chains. Longest chain 23 peptides. Score 0.644 Taking the results from Round 5 Chains 20, Residues 148, Estimated correctness of the model 42.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4883 restraints for refining 2124 atoms. 4311 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1993 (Rfree = 0.000) for 2124 atoms. Found 8 (14 requested) and removed 9 (8 requested) atoms. Cycle 22: After refmac, R = 0.1853 (Rfree = 0.000) for 2118 atoms. Found 14 (14 requested) and removed 9 (8 requested) atoms. Cycle 23: After refmac, R = 0.1783 (Rfree = 0.000) for 2118 atoms. Found 10 (14 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.1730 (Rfree = 0.000) for 2117 atoms. Found 7 (13 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.1518 (Rfree = 0.000) for 2115 atoms. Found 1 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.54 Search for helices and strands: 0 residues in 0 chains, 2163 seeds are put forward NCS extension: 28 residues added (14 deleted due to clashes), 2191 seeds are put forward Round 1: 140 peptides, 22 chains. Longest chain 17 peptides. Score 0.479 Round 2: 157 peptides, 20 chains. Longest chain 18 peptides. Score 0.600 Round 3: 149 peptides, 19 chains. Longest chain 14 peptides. Score 0.585 Round 4: 157 peptides, 21 chains. Longest chain 22 peptides. Score 0.580 Round 5: 162 peptides, 21 chains. Longest chain 24 peptides. Score 0.602 Taking the results from Round 5 Chains 21, Residues 141, Estimated correctness of the model 29.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4810 restraints for refining 2124 atoms. 4267 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1930 (Rfree = 0.000) for 2124 atoms. Found 5 (14 requested) and removed 13 (8 requested) atoms. Cycle 27: After refmac, R = 0.1804 (Rfree = 0.000) for 2109 atoms. Found 9 (13 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.1752 (Rfree = 0.000) for 2109 atoms. Found 10 (13 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.1677 (Rfree = 0.000) for 2108 atoms. Found 7 (13 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1605 (Rfree = 0.000) for 2105 atoms. Found 6 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.57 Search for helices and strands: 0 residues in 0 chains, 2164 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 2203 seeds are put forward Round 1: 138 peptides, 19 chains. Longest chain 18 peptides. Score 0.534 Round 2: 155 peptides, 20 chains. Longest chain 19 peptides. Score 0.591 Round 3: 154 peptides, 19 chains. Longest chain 22 peptides. Score 0.606 Round 4: 148 peptides, 17 chains. Longest chain 23 peptides. Score 0.619 Round 5: 147 peptides, 18 chains. Longest chain 21 peptides. Score 0.595 Taking the results from Round 4 Chains 18, Residues 131, Estimated correctness of the model 34.8 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4756 restraints for refining 2124 atoms. 4214 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1815 (Rfree = 0.000) for 2124 atoms. Found 14 (14 requested) and removed 16 (8 requested) atoms. Cycle 32: After refmac, R = 0.1660 (Rfree = 0.000) for 2115 atoms. Found 4 (14 requested) and removed 11 (8 requested) atoms. Cycle 33: After refmac, R = 0.1497 (Rfree = 0.000) for 2103 atoms. Found 5 (13 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1483 (Rfree = 0.000) for 2100 atoms. Found 1 (13 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1612 (Rfree = 0.000) for 2092 atoms. Found 9 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.50 Search for helices and strands: 0 residues in 0 chains, 2154 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 2190 seeds are put forward Round 1: 126 peptides, 20 chains. Longest chain 17 peptides. Score 0.452 Round 2: 129 peptides, 17 chains. Longest chain 19 peptides. Score 0.534 Round 3: 124 peptides, 14 chains. Longest chain 20 peptides. Score 0.575 Round 4: 125 peptides, 14 chains. Longest chain 20 peptides. Score 0.580 Round 5: 141 peptides, 17 chains. Longest chain 20 peptides. Score 0.589 Taking the results from Round 5 Chains 19, Residues 124, Estimated correctness of the model 25.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4808 restraints for refining 2123 atoms. 4298 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1757 (Rfree = 0.000) for 2123 atoms. Found 14 (14 requested) and removed 16 (8 requested) atoms. Cycle 37: After refmac, R = 0.1670 (Rfree = 0.000) for 2115 atoms. Found 14 (14 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1559 (Rfree = 0.000) for 2116 atoms. Found 11 (14 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.1567 (Rfree = 0.000) for 2115 atoms. Found 10 (13 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.1501 (Rfree = 0.000) for 2114 atoms. Found 5 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.49 Search for helices and strands: 0 residues in 0 chains, 2179 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 2204 seeds are put forward Round 1: 114 peptides, 19 chains. Longest chain 12 peptides. Score 0.410 Round 2: 115 peptides, 15 chains. Longest chain 20 peptides. Score 0.510 Round 3: 118 peptides, 15 chains. Longest chain 20 peptides. Score 0.525 Round 4: 118 peptides, 16 chains. Longest chain 21 peptides. Score 0.502 Round 5: 118 peptides, 15 chains. Longest chain 21 peptides. Score 0.525 Taking the results from Round 5 Chains 16, Residues 103, Estimated correctness of the model 2.3 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4012 reflections ( 99.41 % complete ) and 4822 restraints for refining 2124 atoms. 4385 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1672 (Rfree = 0.000) for 2124 atoms. Found 12 (14 requested) and removed 9 (8 requested) atoms. Cycle 42: After refmac, R = 0.1588 (Rfree = 0.000) for 2125 atoms. Found 7 (14 requested) and removed 10 (8 requested) atoms. Cycle 43: After refmac, R = 0.1541 (Rfree = 0.000) for 2119 atoms. Found 10 (14 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1457 (Rfree = 0.000) for 2120 atoms. Found 10 (14 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1264 (Rfree = 0.000) for 2121 atoms. Found 2 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.49 Search for helices and strands: 0 residues in 0 chains, 2164 seeds are put forward NCS extension: 36 residues added (14 deleted due to clashes), 2200 seeds are put forward Round 1: 112 peptides, 16 chains. Longest chain 20 peptides. Score 0.471 Round 2: 126 peptides, 15 chains. Longest chain 21 peptides. Score 0.563 Round 3: 122 peptides, 15 chains. Longest chain 21 peptides. Score 0.544 Round 4: 124 peptides, 15 chains. Longest chain 21 peptides. Score 0.554 Round 5: 119 peptides, 17 chains. Longest chain 21 peptides. Score 0.484 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 111, Estimated correctness of the model 16.1 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hq7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4012 reflections ( 99.41 % complete ) and 4851 restraints for refining 2124 atoms. 4422 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1513 (Rfree = 0.000) for 2124 atoms. Found 0 (14 requested) and removed 7 (8 requested) atoms. Cycle 47: After refmac, R = 0.1606 (Rfree = 0.000) for 2115 atoms. Found 0 (13 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1489 (Rfree = 0.000) for 2104 atoms. Found 0 (13 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1384 (Rfree = 0.000) for 2097 atoms. TimeTaking 29.28